From e6dbe789aea03cf92e3648eacbb457879d386da5 Mon Sep 17 00:00:00 2001
From: "alice.boizet_cirad.fr" <alice.boizet@cirad.fr>
Date: Thu, 7 Mar 2024 15:12:21 +0000
Subject: [PATCH] Delete sumulation.vba
---
sumulation.vba | 3104 ------------------------------------------------
1 file changed, 3104 deletions(-)
delete mode 100644 sumulation.vba
diff --git a/sumulation.vba b/sumulation.vba
deleted file mode 100644
index 4ede8ca..0000000
--- a/sumulation.vba
+++ /dev/null
@@ -1,3104 +0,0 @@
-'Simulation module for genetic maps and populations
-
-Function gauss()
-'simulated normally-distributed data
-'use: myvalue = gauss * sd + mean
-
-Dim fac As Double, r As Double, V1 As Double, V2 As Double
-
-10 V1 = 2 * Rnd - 1
- V2 = 2 * Rnd - 1
- r = V1 ^ 2 + V2 ^ 2
- If (r >= 1) Then GoTo 10
- fac = Sqr(-2 * Log(r) / r)
- gauss = V2 * fac
-
-End Function
-
-Sub testgauss()
- Dim mean As Variant
- Dim sd As Variant
-
- mean = 0
- sd = 1
- myvalue = gauss * sd + mean
- MsgBox myvalue
-End Sub
-
-Public Sub Simulate_Map()
-'For i = 1 To 1000
-Application.StatusBar = "Simulating map..."
-Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
-ThisWorkbook.Sheets("SimulMap").Activate
-
-Dim SimulatedChromosome As Integer
-Dim NumberOfSimulatedChromosomes As Integer
-Dim SimulatedMarker As Long
-Dim NumberOfSimulatedMarkers As Long
-Dim NumberOfMarkersInThisChromosome As Long
-Dim SimulRow As Long
-Dim SimulatedMapSize As Double
-Dim ChromosomeSize As Double
-Dim MaxVariationPositionRate As Double
-Dim VariationPosition As Double
-Dim SimulatedMarkerPosition As Double
-Dim AverageChromosomeSize As Double
-Dim SimulatedMarkerDensity As Double
-Dim SimulatedChromosomeSizeVariation As Double
-Dim TotalMapSize As Double
-Dim StartChrSize As Double
-Dim GenomeSize As LongLong 'long is max 2,147,483,647
-Dim nbOfMb As LongLong
-Dim bp_cM_ratio As Double
-
-'Map parameters
-NumberOfSimulatedChromosomes = [N9].Value
-SimulatedMapSize = [N10].Value
-SimulatedMarkerDensity = [N11].Value
-SimulatedChromosomeSizeVariation = [N12].Value / 100
-nbOfMb = [j22].Value
-GenomeSize = nbOfMb * 1000000
-bp_cM_ratio = GenomeSize / SimulatedMapSize
-
-If SimulatedMarkerDensity < 0 Then EquallyDispersed = 1
-If [j11] = "yes" Then EquallyDispersed = 2
-
-If EquallyDispersed = 1 Then
- SimulatedMarkerDensity = 0 - SimulatedMarkerDensity
-ElseIf EquallyDispersed = 0 Then
- SimulatedMarkerDensity = SimulatedMarkerDensity + SimulatedMarkerDensity * (NumberOfSimulatedChromosomes / 1000)
- 'gives better results than SimulatedMarkerDensity alone
-ElseIf EquallyDispersed = 2 Then
- If SimulatedMarkerDensity < 0 Then SimulatedMarkerDensity = (0 - SimulatedMarkerDensity)
-End If
-
-MaxVariationPositionRate = [J12]
-
-'Map Simulation
-'Define Chromosome sizes
-AverageChromosomeSize = SimulatedMapSize / NumberOfSimulatedChromosomes
-'ExpectedMarkerNumber = Int(SimulatedMapSize / SimulatedMarkerDensity) + 1
-'ExpectedMarkerNumberPerChromosome = Int(ExpectedMarkerNumber / NumberOfSimulatedChromosomes) + 1
-
-Dim SimulatedMap() As Variant
-ReDim SimulatedMap(1000000, 4)
-
-If [b6] <> "" Then
- msg = "Are you sure you want to clear this simulated map?"
- Style = vbYesNo + vbCritical + vbDefaultButton1
- Title = "Clear results"
- Ctxt = 1000
- response = MsgBox(msg, Style, Title)
- If response = vbYes Then
- ThisWorkbook.Sheets("SimulMap").Range("B6", "F100005").ClearContents
- ThisWorkbook.Sheets("SimulMap").Range("N22:N24").ClearContents
- ThisWorkbook.Sheets("SimulMap").Range("J27:O1000").ClearContents
- ThisWorkbook.Sheets("SimulMap").Range("R22:R25").ClearContents
- Else
- GoTo 1000
- End If
-End If
-
-SimulRow = 0
-NumberOfSimulatedMarkers = 0
-TotalMapSize = 0
-
-[K6] = "Simulating chromosomes... "
-Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
-
-For SimulatedChromosome = 1 To NumberOfSimulatedChromosomes
-
- StartChrSize = 0
- Randomize (Rnd)
- If Rnd > 0.5 Then SimulatedChromosomeSizeVariation = 0 - SimulatedChromosomeSizeVariation
-' Randomize (Rnd)
- ChromosomeSize = AverageChromosomeSize + AverageChromosomeSize * (Rnd * SimulatedChromosomeSizeVariation)
- NumberOfMarkersInThisChromosome = Int(ChromosomeSize / SimulatedMarkerDensity) + 1
- For SimulatedMarker = 1 To NumberOfMarkersInThisChromosome
- NumberOfSimulatedMarkers = NumberOfSimulatedMarkers + 1
- If EquallyDispersed = 1 Then 'fixed positions
- SimulatedMarkerPosition = (ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * (SimulatedMarker - 1)
- ElseIf EquallyDispersed = 0 Then ' random positions
- Randomize (Rnd)
- SimulatedMarkerPosition = Rnd * ChromosomeSize
- ElseIf EquallyDispersed = 2 Then ' semi-random positions
- Randomize (Rnd)
- SimulatedMarkerPosition = (ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * (SimulatedMarker - 1)
- If MaxVariationPositionRate > 0 Then
- If Rnd > 0.5 Then
- VariationPosition = (ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * Rnd * MaxVariationPositionRate
- Else
- VariationPosition = 0 - ((ChromosomeSize / (NumberOfMarkersInThisChromosome - 1)) * Rnd * MaxVariationPositionRate)
- End If
- Else
- VariationPosition = 0
- End If
- SimulatedMarkerPosition = SimulatedMarkerPosition + VariationPosition
- End If
- ''Debug.Print SimulatedChromosome
- SimulatedMap(SimulRow, 0) = SimulatedChromosome
- SimulatedMap(SimulRow, 1) = NumberOfSimulatedMarkers
- fakeMkphysicalPosition = Int(SimulatedMarkerPosition * bp_cM_ratio)
-' SimulatedMap(SimulRow, 2) = "Chr" & SimulatedChromosome & "_M" & SimulatedMarker
- SimulatedMap(SimulRow, 2) = "Chr" & SimulatedChromosome & "_" & fakeMkphysicalPosition
-
- If SimulatedMarker = 1 Then
- SimulatedMap(SimulRow, 3) = 0
- ElseIf SimulatedMarker = NumberOfMarkersInThisChromosome Then
- SimulatedMap(SimulRow, 3) = ChromosomeSize
-' SimulatedMap(SimulRow, 3) = Format(ChromosomeSize, "####.00")
- Else
- SimulatedMap(SimulRow, 3) = SimulatedMarkerPosition
-' SimulatedMap(SimulRow, 3) = Format(SimulatedMarkerPosition, "####.00") 'very slow
- End If
-' 'If SimulatedMarkerPosition > StartChrSize Then StartChrSize = SimulatedMarkerPosition
- SimulRow = SimulRow + 1
- Next SimulatedMarker
- 'FinalChromosomeSize = StartChrSize
- TotalMapSize = TotalMapSize + ChromosomeSize
- Cells(26 + SimulatedChromosome, 10) = SimulatedChromosome
- Cells(26 + SimulatedChromosome, 11) = Format(ChromosomeSize, "####.00")
- Cells(26 + SimulatedChromosome, 12) = NumberOfMarkersInThisChromosome
- Cells(26 + SimulatedChromosome, 14) = Format(ChromosomeSize / NumberOfMarkersInThisChromosome, "####.000")
-' chrcM_Mbp = ChromosomeSize / (fakeMkphysicalPosition / 1000000)
-' Cells(26 + SimulatedChromosome, 15) = Format(chrcM_Mbp, "####.00")
-Next SimulatedChromosome
-
-[K6] = ""
-
-[N22] = TotalMapSize
-[N23] = NumberOfSimulatedMarkers
-[N24] = Format(TotalMapSize / NumberOfSimulatedMarkers, "####.000")
-
-[R22] = [N9]
-[r23] = [N10]
-[R24] = [N11]
-[R25] = [N12]
-
- Cells(26, 10) = "Chr"
- Cells(26, 11) = "cM"
- Cells(26, 12) = "Mk"
- Cells(26, 14) = "density"
-
-'Application.StatusBar = "Writing map..."
-'Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
-'ThisWorkbook.Sheets("SimulMap").Activate
-'Range("B6:E100005").Select
-'Selection.ClearContents
-
-ThisWorkbook.Sheets("SimulMap").Range("B6").Resize(NumberOfSimulatedMarkers, 4) = SimulatedMap
-Erase SimulatedMap
-
-'Application.StatusBar = "Sorting map by position..."
-'Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
-
-Range("B6:E100005").Select
-Selection.Sort Key1:=Range("B6"), Order1:=xlAscending, Key2:=Range("E6") _
-, Order2:=xlAscending, Header:=xlGuess, OrderCustom:=1, MatchCase:= _
-False, Orientation:=xlTopToBottom
-
-[b6].Select
-
-'Application.StatusBar = "Sorting map by locus number..."
-'Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
-
-Range("C6:D100000").Select
-Selection.Sort Key1:=Range("C6"), Order1:=xlAscending, Header:=xlGuess, _
- OrderCustom:=1, MatchCase:=False, Orientation:=xlTopToBottom
-
-Range("N22").Select
-Application.ScreenUpdating = True
-'Next i
-1000
-Application.StatusBar = False
-End Sub
-
-
-Public Sub Chr_Start_at_0()
-Application.ScreenUpdating = False
-
-If [b6] <> "" Then
- msg = "Are you sure you want to do this? All marker positions will be recalculated in order to let chromosomes start at position 0"
- Style = vbYesNo + vbCritical + vbDefaultButton1
- Title = "Start at 0"
- Ctxt = 1000
- response = MsgBox(msg, Style, Title)
- If response = vbNo Then
- GoTo 1000
- End If
-End If
-
-ThisWorkbook.Sheets("SimulMap").Activate
-
-'first, counts the chr parameters (same than Read_Chr_Simulated)
-Range("B6", Range("B1048576").End(xlUp)).Select
-NbOfRows = Selection.Rows.Count
-
-NumbOfMarkInChrTotal = 0
-TotalMapSize = 0
-NumberOfChr = 0
-For i = 6 To NbOfRows + 6
- If Cells(i + 1, 2) <> Cells(i, 2) Then 'new chr is detected
- NumberOfChr = NumberOfChr + 1
- Cells(26 + Cells(i, 2), 10) = Cells(i, 2) 'chr number
- ChrSize = Cells(i, 5)
- Cells(26 + Cells(i, 2), 11) = ChrSize 'chr size
- TotalMapSize = TotalMapSize + Cells(i, 5)
- NumbOfMarkInChr = i - 5 - NumbOfMarkInChrTotal
- Cells(26 + Cells(i, 2), 12) = NumbOfMarkInChr
- MarkerDensity = ChrSize / NumbOfMarkInChr
- Cells(26 + Cells(i, 2), 14) = MarkerDensity
- NumbOfMarkInChrTotal = NumbOfMarkInChrTotal + NumbOfMarkInChr
- End If
-Next
-[N22] = TotalMapSize
-[N23] = NumbOfMarkInChrTotal
-[N24] = TotalMapSize / NumbOfMarkInChrTotal
-[R22] = NumberOfChr
-
-'second, reformats the marker positions to start at 0
-firstRow = 6
-NbOfProcessedRows = 0
-For chromosome = 1 To NumberOfChr
- NumbOfMarkInChr = Cells(26 + chromosome, 12)
- FirstPosition = Cells(NbOfProcessedRows + 6, 5)
- For mark = 1 To NumbOfMarkInChr
- Cells(NbOfProcessedRows + mark + 5, 5) = Cells(NbOfProcessedRows + mark + 5, 5) - FirstPosition
- Next
- NbOfProcessedRows = NbOfProcessedRows + NumbOfMarkInChr
-Next chromosome
-
-'third, re-reads and writes the chr parameters
-NumbOfMarkInChrTotal = 0
-TotalMapSize = 0
-NumberOfChr = 0
-For i = 6 To NbOfRows + 6
- If Cells(i + 1, 2) <> Cells(i, 2) Then 'new chr is detected
- NumberOfChr = NumberOfChr + 1
- Cells(26 + Cells(i, 2), 10) = Cells(i, 2) 'chr number
- ChrSize = Cells(i, 5)
- Cells(26 + Cells(i, 2), 11) = ChrSize 'chr size
- TotalMapSize = TotalMapSize + Cells(i, 5)
- NumbOfMarkInChr = i - 5 - NumbOfMarkInChrTotal
- Cells(26 + Cells(i, 2), 12) = NumbOfMarkInChr
- MarkerDensity = ChrSize / NumbOfMarkInChr
- Cells(26 + Cells(i, 2), 14) = MarkerDensity
- NumbOfMarkInChrTotal = NumbOfMarkInChrTotal + NumbOfMarkInChr
- End If
-Next
-[N22] = TotalMapSize
-[N23] = NumbOfMarkInChrTotal
-[N24] = TotalMapSize / NumbOfMarkInChrTotal
-[R22] = NumberOfChr
-
-1000 [N22].Select
-Application.CutCopyMode = False
-Application.ScreenUpdating = True
-End Sub
-
-
-Sub Add_Trait_To_Population_In_Data()
-
-Application.ScreenUpdating = False
-Init
-
-popType = Sheets("Data").[D4]
-popsize = Sheets("Data").[D5]
-nbloci = Sheets("Data").[D6]
-NbTraits = Sheets("Data").[D7]
-
-nbHeaders = 15
-
-outcellrow = nbloci + NbTraits + nbHeaders + 1
-
-mkQTL1 = ThisWorkbook.Sheets("SimulMap").[R39]
-NbOfTraitsToAdd = ThisWorkbook.Sheets("SimulMap").[R40]
-
-Dim SimulatedTrait() As Variant
-ReDim SimulatedTrait(1 To NbOfTraitsToAdd, 1 To popsize + 2)
-
-MeanAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R31]
-MeanAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R32]
-MeanBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R33]
-VarCoeffAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R34]
-VarCoeffAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R35]
-VarCoeffBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R36]
-SD_AA_QTL1 = MeanAA_QTL1 * VarCoeffAA_QTL1
-SD_AB_QTL1 = MeanAB_QTL1 * VarCoeffAB_QTL1
-SD_BB_QTL1 = MeanBB_QTL1 * VarCoeffBB_QTL1
-
-Randomize (Rnd)
-
-If popType = "SSD" Or popType = "DH" Then
- For j = 1 To NbOfTraitsToAdd
- SimulatedTrait(j, 1) = NbTraits + j
- SimulatedTrait(j, 2) = "SimulatedTrait_" & NbTraits + j
- For i = 1 To popsize
- Genotype = Data(i - 1, mkQTL1 - 1)
- If Genotype = "A" Then
- myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
- SimulatedTrait(j, i + 2) = Format(myAAvalue, "###.00")
- ElseIf Genotype = "B" Then
- myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
- SimulatedTrait(j, i + 2) = Format(myBBvalue, "###.00")
- Else
- SimulatedTrait(j, i + 2) = "-"
- End If
- Next
- Next
-ElseIf popType = "BC1" Then
- For j = 1 To NbOfTraitsToAdd
- SimulatedTrait(j, 1) = NbTraits + j
- SimulatedTrait(j, 2) = "SimulatedTrait_" & NbTraits + j
- For i = 1 To popsize
- Genotype = Data(i - 1, mkQTL1 - 1)
- If Genotype = "A" Then
- myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
- SimulatedTrait(j, i + 2) = Format(myAAvalue, "###.00")
- ElseIf Genotype = "H" Then
- myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
- SimulatedTrait(j, i + 2) = Format(myABvalue, "###.00")
- Else
- SimulatedTrait(j, i + 2) = "-"
- End If
- Next
- Next
-ElseIf popType = "F2" Then
- For j = 1 To NbOfTraitsToAdd
- SimulatedTrait(j, 1) = NbTraits + j
- SimulatedTrait(j, 2) = "SimulatedTrait_" & NbTraits + j
- For i = 1 To popsize
- Genotype = Data(i - 1, mkQTL1 - 1)
- If Genotype = "H" Then
- myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
- SimulatedTrait(j, i + 2) = Format(myABvalue, "###.00")
- ElseIf Genotype = "A" Then
- myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
- SimulatedTrait(j, i + 2) = Format(myAAvalue, "###.00")
- ElseIf Genotype = "B" Then
- myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
- SimulatedTrait(j, i + 2) = Format(myBBvalue, "###.00")
- Else
- SimulatedTrait(j, i + 2) = "-"
- End If
- Next
- Next
-End If
-
-
-Sheets("Data").Activate
-Cells(outcellrow, 1).Resize(NbOfTraitsToAdd, popsize + 2) = SimulatedTrait
-
-Sheets("Data").[D7] = NbTraits + NbOfTraitsToAdd
-End Sub
-
-Sub Add_Random_Trait_To_Population_In_Data()
-
-Application.ScreenUpdating = False
-Init
-
-popType = Sheets("Data").[D4]
-popsize = Sheets("Data").[D5]
-nbloci = Sheets("Data").[D6]
-NbTraits = Sheets("Data").[D7]
-
-nbHeaders = 15
-
-outcellrow = nbloci + NbTraits + nbHeaders + 1
-
-NbOfTraitsToAdd = ThisWorkbook.Sheets("SimulMap").[R43]
-
-Dim SimulatedTrait() As Variant
-ReDim SimulatedTrait(1 To NbOfTraitsToAdd, 1 To popsize + 2)
-
-MeanAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R31]
-MeanAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R32]
-MeanBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R33]
-VarCoeffAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R34]
-VarCoeffAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R35]
-VarCoeffBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R36]
-SD_AA_QTL1 = MeanAA_QTL1 * VarCoeffAA_QTL1
-SD_AB_QTL1 = MeanAB_QTL1 * VarCoeffAB_QTL1
-SD_BB_QTL1 = MeanBB_QTL1 * VarCoeffBB_QTL1
-
-Randomize (Rnd)
-
-For j = 1 To NbOfTraitsToAdd
- SimulatedTrait(j, 1) = NbTraits + j
- SimulatedTrait(j, 2) = "RandomTrait_" & NbTraits + j
- For i = 1 To popsize
- myvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
- SimulatedTrait(j, i + 2) = Format(myvalue, "###.00")
- Next
-Next
-
-Sheets("Data").Activate
-Cells(outcellrow, 1).Resize(NbOfTraitsToAdd, popsize + 2) = SimulatedTrait
-
-Sheets("Data").[D7] = NbTraits + NbOfTraitsToAdd
-End Sub
-
-Public Sub Read_Simulation_Parameters()
-'only for autobatchmap
-SimulatedPopulationType = VirtualMap(16, 14) 'ONLY BC1 & F2 pops at this stage
-
-SimulatedPopulationSize = VirtualMap(17, 14)
-
-MapFunctionSimul = VirtualMap(18, 14)
-
-ChromosomeSDL1 = VirtualMap(9, 18)
-If ChromosomeSDL1 > 0 Then
- PositionSDL1 = VirtualMap(10, 18)
- ViabU = VirtualMap(15, 18) 'differential viability fA/fB for SDL1
- SDL1AbsoluteNumber = 0
- For i = 1 To ChromosomeSDL1 - 1
- SDL1AbsoluteNumber = SDL1AbsoluteNumber + VirtualMap(26 + i, 12)
- Next
- SDL1AbsoluteNumber = SDL1AbsoluteNumber + PositionSDL1
-End If
-
-ChromosomeSDL2 = VirtualMap(11, 18)
-If ChromosomeSDL2 > 0 Then
- PositionSDL2 = VirtualMap(12, 18)
- ViabV = VirtualMap(17, 18) 'differential viability fA/fB for SDL2
- SDL2AbsoluteNumber = 0
- For i = 1 To ChromosomeSDL2 - 1
- SDL2AbsoluteNumber = SDL2AbsoluteNumber + VirtualMap(26 + i, 12)
- Next
- SDL2AbsoluteNumber = SDL2AbsoluteNumber + PositionSDL2
-End If
-
-NumberOfSimulatedTraits = VirtualMap(19, 14)
-NumberOfSimulatedMarkers = VirtualMap(23, 14)
-NumberOfSimulatedChromosomes = VirtualMap(22, 18)
-RandomErrorRate = VirtualMap(18, 10)
-RandomMissingDataRate = VirtualMap(19, 10)
-
-End Sub
-
-Public Sub Simulate_Population_From_Map()
-
-'version for excel 2007+ ONLY
-'On Error GoTo 900
-Dim SegDistortersAreIndependant As Boolean, SDL2ConditionalToSDL1 As Boolean
-Dim genotypeNames() As Variant
-
-Application.ScreenUpdating = False
-
-Read_Parameters
-
-SegDistortersAreIndependant = True
-SDL2ConditionalToSDL1 = False
-
-'QTL1 parameters
-ChrQTL1 = ThisWorkbook.Sheets("SimulMap").[R29]
-MarkerNumberQTL1 = ThisWorkbook.Sheets("SimulMap").[R30]
-MeanAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R31]
-MeanAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R32]
-MeanBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R33]
-VarCoeffAA_QTL1 = ThisWorkbook.Sheets("SimulMap").[R34]
-VarCoeffAB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R35]
-VarCoeffBB_QTL1 = ThisWorkbook.Sheets("SimulMap").[R36]
-SD_AA_QTL1 = MeanAA_QTL1 * VarCoeffAA_QTL1
-SD_AB_QTL1 = MeanAB_QTL1 * VarCoeffAB_QTL1
-SD_BB_QTL1 = MeanBB_QTL1 * VarCoeffBB_QTL1
-Mean_QTL1_for_Random_Backcross = 0.5 * (MeanAA_QTL1 + MeanAB_QTL1)
-SD_AA_QTL1_for_Random_Backcross = Mean_QTL1_for_Random_Backcross * 0.5 * (VarCoeffAA_QTL1 + VarCoeffAB_QTL1)
-Mean_QTL1_for_Random_DH = 0.5 * (MeanAA_QTL1 + MeanBB_QTL1)
-Mean_QTL1_for_Random_F2 = 0.5 * (MeanAA_QTL1 + MeanBB_QTL1)
-
-If AutoBatchMapOn = 0 Then Application.StatusBar = "Starting..."
-
-'Population Parameters
-Sheets("SimulMap").[K6] = "Simulating population... ": Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
-
-If AutoBatchMapOn = 1 Then
- NumberOfSimulatedPopulations = 1
- Read_Simulation_Parameters
-Else
- ThisWorkbook.Sheets("SimulMap").Activate
- NumberOfSimulatedPopulations = ThisWorkbook.Sheets("SimulMap").[N15]
- saveInFiles = ThisWorkbook.Sheets("SimulMap").[O15]
- VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
-
- SimulatedPopulationType = ThisWorkbook.Sheets("SimulMap").[N16] 'ONLY BC1 & F2 pops at this stage
- If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" _
- And SimulatedPopulationType <> "BC2F1" And SimulatedPopulationType <> "SSD" _
- Then MsgBox "BC1 or F2 or SSD populations only, sorry.": GoTo 1000
- SimulatedPopulationSize = ThisWorkbook.Sheets("SimulMap").[N17] 'NOT more than 508 individuals at this stage
-' If MaxNumberOfColumns = 256 Then
- If SimulatedPopulationSize > 16382 And NumberOfSimulatedPopulations = 1 Then
- SimulatedPopulationSize = 1
- MsgBox "I can't simulate more than 16382 individuals. If you need more individuals, please simulate 2 or more populations; this will generate Mapmaker/EXP compatible files that you can analyze using the BatchMap command."
- End If
-' End If
-
- ChromosomeSDL1 = ThisWorkbook.Sheets("SimulMap").[R9]
- If ChromosomeSDL1 > 0 Then
- PositionSDL1 = ThisWorkbook.Sheets("SimulMap").[R10]
- ViabU = ThisWorkbook.Sheets("SimulMap").[R15] 'differential viability fA/fB for SDL1 (BC1 or F2) - gametic selection
- ViabU1 = ThisWorkbook.Sheets("SimulMap").[R16] 'differential viability fAA/fBB for SDL1 (F2) - zygotic selection
- ViabU2 = ThisWorkbook.Sheets("SimulMap").[R17] 'differential viability fAB/fBB for SDL1 (F2) - zygotic selection
- ViabU3 = ViabU2 / ViabU1 'differential viability fAB/fAA for SDL1 (F2) - zygotic selection
- SDL1AbsoluteNumber = 0
- For i = 1 To ChromosomeSDL1 - 1
- SDL1AbsoluteNumber = SDL1AbsoluteNumber + ThisWorkbook.Sheets("SimulMap").Cells(26 + i, 12)
- Next
- SDL1AbsoluteNumber = SDL1AbsoluteNumber + PositionSDL1
- End If
-
- ChromosomeSDL2 = ThisWorkbook.Sheets("SimulMap").[R11]
- If ChromosomeSDL2 > 0 Then
- PositionSDL2 = ThisWorkbook.Sheets("SimulMap").[R12]
- ViabV = ThisWorkbook.Sheets("SimulMap").[R18]
- ViabV1 = ThisWorkbook.Sheets("SimulMap").[R19]
- ViabV2 = ThisWorkbook.Sheets("SimulMap").[R20]
- ViabV3 = ViabV2 / ViabV1 'differential viability fAB/fAA for SDL2 (F2) - zygotic selection
- SDL2AbsoluteNumber = 0
- For i = 1 To ChromosomeSDL2 - 1
- SDL2AbsoluteNumber = SDL2AbsoluteNumber + Cells(26 + i, 12)
- Next
- SDL2AbsoluteNumber = SDL2AbsoluteNumber + PositionSDL2
- End If
-
- 'F2 options for segregation distortion
- SelTypeGameticMaleSDL1 = ThisWorkbook.Sheets("SimulMap").[X15]
- SelTypeGameticFemaleSDL1 = ThisWorkbook.Sheets("SimulMap").[X16]
- SelTypeZygoticSDL1 = ThisWorkbook.Sheets("SimulMap").[X17]
- SelTypeGameticMaleSDL2 = ThisWorkbook.Sheets("SimulMap").[X18]
- SelTypeGameticFemaleSDL2 = ThisWorkbook.Sheets("SimulMap").[X19]
- SelTypeZygoticSDL2 = ThisWorkbook.Sheets("SimulMap").[X20]
-
- NumberOfSimulatedTraits = 1
- NumberOfSimulatedRandomTraits = ThisWorkbook.Sheets("SimulMap").[N19]
-
- nbOfSupPops = 1
- If NumberOfSimulatedPopulations > 1 And saveInFiles = True Then
- OperatingSystem = ThisWorkbook.Sheets("hide").Cells(8, 1)
- OperatingSystem = UCase(Left(OperatingSystem, 3))
- If OperatingSystem = "WIN" Then
- FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="Text Files (*.txt), *.txt")
- ElseIf OperatingSystem = "MAC" Then
- FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="TEXT")
- End If
- If FileSaveName = False Then GoTo 1000
-
- LengthOfPath = Len(FileSaveName)
- OutputPath = Left(FileSaveName, LengthOfPath - 9)
- 'MsgBox "The output folder will be " & Chr(13) & OutputPath
- ElseIf NumberOfSimulatedPopulations > 1 And saveInFiles = False Then
- nbOfSupPops = NumberOfSimulatedPopulations
- subPopSize = Int(SimulatedPopulationSize / nbOfSupPops)
- remainderSubPopSize = SimulatedPopulationSize - nbOfSupPops * subPopSize
- NumberOfSimulatedPopulations = 1
-
- ReDim genotypeNames(1 To 1, 1 To SimulatedPopulationSize)
- outcolsub = 1
- For subPop = 1 To nbOfSupPops
- For mygenot = 1 To subPopSize
- genotypeNames(1, outcolsub) = "pop" & subPop & "_genot" & mygenot
- outcolsub = outcolsub + 1
- Next
- Next
- If remainderSubPopSize > 0 Then
- genotnumber = subPopSize + 1
- For mygenot = nbOfSupPops * subPopSize + 1 To SimulatedPopulationSize
- genotypeNames(1, mygenot) = "pop" & nbOfSupPops & "_genot" & genotnumber
- genotnumber = genotnumber + 1
- Next
- End If
- MapFunctionSimul = ThisWorkbook.Sheets("SimulMap").[N18]
- ElseIf NumberOfSimulatedPopulations = 1 And saveInFiles = False Then
- ReDim genotypeNames(1 To 1, 1 To SimulatedPopulationSize)
- For mygenot = 1 To SimulatedPopulationSize
- genotypeNames(1, mygenot) = "pop1" & "_genot" & mygenot
- Next
-
- MapFunctionSimul = ThisWorkbook.Sheets("SimulMap").[N18]
-
- End If
-
-
- 'Reading map parameters
- Application.StatusBar = "Reading map parameters"
-
- 'TotalMapSize = [N22]
- NumberOfSimulatedMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
- NumberOfSimulatedChromosomes = ThisWorkbook.Sheets("SimulMap").[R22]
- RandomErrorRate = [j18]
- RandomMissingDataRate = [j19]
-
-End If
-'If NumberOfSimulatedPopulations > 1 And AutoBatchMapOn = 0 Then ' simulate genotypes and write in txt files
-
-Dim SimulatedGenotypes() As Variant
-
-Randomize (Rnd)
-
-For SimulatedPopulation = 1 To NumberOfSimulatedPopulations
-
- If AutoBatchMapOn = 0 Then Application.StatusBar = "Simulating population " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations
-
- 'ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedPopulationSize + 1) As Variant
- ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits + 1, SimulatedPopulationSize + 1)
-
-'BACKCROSS
- If SimulatedPopulationType = "BC1" Then 'fake, because does not simulate properly the 4 possible gametes. However gives correct RFs (+ or -)
-
- For SimulatedGenotype = 1 To SimulatedPopulationSize
-10
- If AutoBatchMapOn = 0 Then Application.StatusBar = "Pop " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations & ": Genot " & SimulatedGenotype & " of " & SimulatedPopulationSize
- StartRow = 1
-
- For chromosome = 1 To NumberOfSimulatedChromosomes
-
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- MarkerPositionOld = 0
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
- SimulatedGenotypes(StartRow, SimulatedGenotype) = Genotype
- For Marker = 2 To NbOfMrksInChr
- 'Application.StatusBar = "Pop " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations & " - Chr " & chromosome & " - Mk " & marker
-
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- 'IntervalWithPreviousMarkerInRF = IntervalWithPreviousMarker / 100
-
- If Rnd <= IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If Genotype = "A" Then
- Genotype = "H"
- ElseIf Genotype = "H" Then
- Genotype = "A"
- End If
- End If
-
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
-
- 'simulate non-random trait
- If ChrQTL1 = chromosome Then
- If Marker = MarkerNumberQTL1 Then
- If Genotype = "A" Then
- myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myAAvalue, "###.00")
- ElseIf Genotype = "H" Then
- myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myABvalue, "###.00")
- End If
- End If
- End If
- MarkerPositionOld = MarkerPosition
- Next 'Marker
- StartRow = StartRow + NbOfMrksInChr
- Next 'chromosome
-
- GameteIsDead = 0
- GameteIsDeadSDL1 = 0
- GameteIsDeadSDL2 = 0
-
- If ChromosomeSDL1 > 0 Then ' there is a segregation distorter
- FreqA = ViabU / (1 + ViabU) 'final frequency, 0 to 0.5
- 'SurvivalA = FreqA * 2 '0 to 1
- FreqH = 1 / (1 + ViabU) 'final frequency
- 'SurvivalH = FreqH * 2
- myRandkillSDL1 = Rnd
- If ViabU < 1 Then 'selection against AA genotypes or A gametes
-' If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > FreqA Then 'you're dead, gamete A!
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkillSDL1 > ViabU Then 'you're dead, gamete A!
- GameteIsDeadSDL1 = 1
- End If
- ElseIf ViabU > 1 Then 'selection against H genotypes or B gametes
-' If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > FreqH Then ' you're dead, gamete B!
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkillSDL1 > 1 / ViabU Then ' you're dead, gamete B!
- GameteIsDeadSDL1 = 1
- End If
- End If
- End If
-
- If ChromosomeSDL2 > 0 Then ' there is another segregation distorter
- FreqA = ViabV / (1 + ViabV) 'final frequency, 0 to 0.5
- 'SurvivalA = FreqA * 2 '0 to 1
- FreqH = 1 / (1 + ViabV) 'final frequency
- 'SurvivalH = FreqH * 2
- myRandkillSDL2 = Rnd
- If ViabV < 1 Then 'selection against AA genotypes or A gametes
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkillSDL2 > ViabV Then '... you're dead, gamete A!
- GameteIsDeadSDL2 = 1
- End If
- ElseIf ViabV > 1 Then 'selection against H genotypes or B gametes
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkillSDL2 > 1 / ViabV Then '... you're dead, gamete B!
- GameteIsDeadSDL2 = 1
- End If
- End If
- End If
-
- If SegDistortersAreIndependant = True Then 'no epistasis
- If GameteIsDeadSDL1 = 1 Or GameteIsDeadSDL2 = 1 Then GameteIsDead = 1
- ElseIf SegDistortersAreIndependant = False Then 'both death required, epistasis
- If SDL2ConditionalToSDL1 = True Then
- If GameteIsDeadSDL1 = 0 And GameteIsDeadSDL2 = 1 Then GameteIsDead = 1
- ElseIf SDL2ConditionalToSDL1 = False Then
- If GameteIsDeadSDL1 = 1 And GameteIsDeadSDL2 = 1 Then GameteIsDead = 1
- End If
- End If
-
- If GameteIsDead = 1 Then GoTo 10
-
- 'random traits (normally distributed)
- For mytrait = 1 To NumberOfSimulatedRandomTraits
- myvalue = gauss * SD_AA_QTL1_for_Random_Backcross + Mean_QTL1_for_Random_Backcross
- SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, SimulatedGenotype) = Format(myvalue, "###.00")
-' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
- Next 'mytrait
-
- Next 'SimulatedGenotype
-
- If RandomErrorRate > 0 And RandomErrorRate <= 1 Then
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For Marker = 1 To NbOfMrksInChr
- If Rnd >= (1 - RandomErrorRate) Then
- If SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A" Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
- ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H" Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
- End If
- End If
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- Next SimulatedGenotype
- End If
-
- If RandomMissingDataRate > 0 And RandomMissingDataRate <= 1 Then
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For Marker = 1 To NbOfMrksInChr
- If Rnd >= 1 - RandomMissingDataRate Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "-"
- End If
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- Next SimulatedGenotype
- End If
-
- For mytrait = 1 To NumberOfSimulatedRandomTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, 0) = "RandomQTrait_" & mytrait
- Next 'mytrait
-
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, 0) = "SimulatedQTrait_1"
-
-
-'BACKCROSS - RARE
- ElseIf SimulatedPopulationType = "BC1bizarre" Then 'try to mimic better meiosis behavior
-
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- MarkerPositionOld = 0
- Marker = StartRow
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
- SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
- If Rnd > 0.5 Then 'Recombined Gamete
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld 'in cM
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- 'Randomize (Rnd)
- If Rnd > 1 - 2 * IntervalWithPreviousMarkerInRF Then 'a recombination occurred - seems to generate too many 2ble recombinations
- If Genotype = "A" Then
- Genotype = "H"
- ElseIf Genotype = "H" Then
- Genotype = "A"
- End If
- End If
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- MarkerPositionOld = MarkerPosition
- Next 'Marker
- Else 'parental gamete
- For Marker = 2 To NbOfMrksInChr
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- Next 'Marker
- End If
- StartRow = StartRow + NbOfMrksInChr
- Next 'chromosome
-
- Next 'SimulatedGenotype
-
-
-'BC2F1
- ElseIf SimulatedPopulationType = "BC2F1" Then
-' A FINIR
-
- BC2FamilySize = 4 ' a mettre en variable
-
- BC2PopulationSize = SimulatedPopulationSize * BC2FamilySize
- For SimulatedGenotype = 1 To SimulatedPopulationSize
-50
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- MarkerPositionOld = 0
- Marker = StartRow
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
- SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If Genotype = "A" Then
- Genotype = "H"
- ElseIf Genotype = "H" Then
- Genotype = "A"
- End If
- End If
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- MarkerPositionOld = MarkerPosition
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- ' For mytrait = 1 To NumberOfSimulatedRandomTraits
- ' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
- ' Next mytrait
- Next SimulatedGenotype
- ' For mytrait = 1 To NumberOfSimulatedRandomTraits
- ' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
- ' Next mytrait
-
-
-
-' F2 POPULATION
- ElseIf SimulatedPopulationType = "F2" Then
-
- For SimulatedGenotype = 1 To SimulatedPopulationSize
-100
- StartRow = 1
- Gamete1_Is_Dead = 0
- Gamete2_Is_Dead = 0
- Zygote_Is_Dead = 0
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- MarkerPositionOld = 0
- 'Randomize (Rnd)
- If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
- 'Randomize (Rnd)
- If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
- Marker = StartRow
- If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "A"
- If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "B"
- If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
- If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
-
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
-
- 'male gamete
- 'Randomize (Rnd)
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If genotype1 = "A" Then
- genotype1 = "B"
- ElseIf genotype1 = "B" Then
- genotype1 = "A"
- End If
- End If
- 'selection on male gamete (SDL 1)
- If SelTypeGameticMaleSDL1 = "x" Then
- If chromosome = ChromosomeSDL1 Then
- If Marker = PositionSDL1 Then
- ''Debug.Print "SDL1 - gam sel", ViabU
- myRandkill = Rnd
- If ViabU < 1 Then 'selection against A gametes
- If genotype1 = "A" And myRandkill > ViabU Then 'gamete A dies
- Gamete1_Is_Dead = 1
- ''Debug.Print "killed"
- End If
- ElseIf ViabU > 1 Then 'selection against B gametes
- If genotype1 = "B" And myRandkill > 1 / ViabU Then 'gamete B dies
- Gamete1_Is_Dead = 1
- ''Debug.Print "killed"
- End If
- End If
- End If
- End If
- End If
- If SelTypeGameticMaleSDL2 = "x" Then
- 'selection on male gamete (SDL 2)
- If chromosome = ChromosomeSDL2 Then
- If Marker = PositionSDL2 Then
- myRandkill = Rnd
- If ViabV < 1 Then 'selection against A gametes
- If genotype1 = "A" And myRandkill > ViabV Then 'gamete A dies
- Gamete1_Is_Dead = 1
- End If
- ElseIf ViabU > 1 Then 'selection against B gametes
- If genotype1 = "B" And myRandkill > 1 / ViabV Then 'gamete B dies
- Gamete1_Is_Dead = 1
- End If
- End If
- End If
- End If
- End If
- 'female gamete
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If genotype2 = "A" Then
- genotype2 = "B"
- ElseIf genotype2 = "B" Then
- genotype2 = "A"
- End If
- End If
-' Gamete2_Is_Dead = 0
- 'selection
- If SelTypeGameticFemaleSDL1 = "x" Then
- If chromosome = ChromosomeSDL1 Then
- If Marker = PositionSDL1 Then
- myRandkill = Rnd
- If ViabU < 1 Then 'selection against A gametes
- If genotype2 = "A" And myRandkill > ViabU Then 'gamete A dies
- Gamete2_Is_Dead = 1
- End If
- ElseIf ViabU > 1 Then 'selection against B gametes
- If genotype2 = "B" And myRandkill > 1 / ViabU Then 'gamete B dies
- Gamete2_Is_Dead = 1
- End If
- End If
- End If
- End If
- End If
- If SelTypeGameticFemaleSDL2 = "x" Then
- If chromosome = ChromosomeSDL2 Then
- If Marker = PositionSDL2 Then
- myRandkill = Rnd
- If ViabV < 1 Then 'selection against A gametes
- If genotype2 = "A" And myRandkill > ViabV Then 'gamete A dies
- Gamete2_Is_Dead = 1
- End If
- ElseIf ViabU > 1 Then 'selection against B gametes
- If genotype2 = "B" And myRandkill > 1 / ViabV Then 'gamete B dies
- Gamete2_Is_Dead = 1
- End If
- End If
- End If
- End If
- End If
- 'mating or selfing
- If genotype1 = "A" And genotype2 = "A" Then Genotype = "A"
- If genotype1 = "B" And genotype2 = "B" Then Genotype = "B"
- If genotype1 = "A" And genotype2 = "B" Then Genotype = "H"
- If genotype1 = "B" And genotype2 = "A" Then Genotype = "H"
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- 'simulate non-random trait
- If ChrQTL1 = chromosome Then
- If Marker = MarkerNumberQTL1 Then
- If Genotype = "H" Then
- myABvalue = gauss * SD_AB_QTL1 + MeanAB_QTL1
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myABvalue, "###.00")
- ElseIf Genotype = "A" Then
- myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myAAvalue, "###.00")
- ElseIf Genotype = "B" Then
- myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myBBvalue, "###.00")
- End If
- End If
- End If
- MarkerPositionOld = MarkerPosition
-
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
-
- Next chromosome
-
- If Gamete1_Is_Dead = 1 Then GoTo 100
- If Gamete2_Is_Dead = 1 Then GoTo 100
-
- 'eliminate zygotes
-
- If ChromosomeSDL1 > 0 Then ' there is a segregation distorter
- myRandkill = Rnd
- If ViabU1 < 1 Then 'selection against AA genotype relative to BB genotype
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > ViabU1 Then 'AA killed
- Zygote_Is_Dead = 1
- End If
- ElseIf ViabU1 > 1 Then 'selection against AA genotype relative to BB genotype
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabU1 Then 'sorry, bad luck... you're dead, gamete B!
- Zygote_Is_Dead = 1
- End If
- End If
- If ViabU2 < 1 Then 'selection against AB genotype relative to BB genotype
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabU2 Then 'AA killed
- Zygote_Is_Dead = 1
- End If
- ElseIf ViabU2 > 1 Then 'selection against BB genotype versus AB genotype
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabU2 Then 'sorry, bad luck... you're dead, gamete B!
- Zygote_Is_Dead = 1
- End If
- End If
- If ViabU3 < 1 Then 'selection against AB genotype relative to AA genotype
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabU3 Then 'AA killed
- Zygote_Is_Dead = 1
- End If
- ElseIf ViabU3 > 1 Then 'selection against AA genotype versus AB genotype
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > 1 / ViabU3 Then 'sorry, bad luck... you're dead, gamete B!
- Zygote_Is_Dead = 1
- End If
- End If
- End If
-
- If ChromosomeSDL2 > 0 Then ' there is a segregation distorter
- myRandkill = Rnd
- If ViabV1 < 1 Then 'selection against AA genotype relative to BB genotype
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > ViabV1 Then 'AA killed
- Zygote_Is_Dead = 1
- End If
- ElseIf ViabV1 > 1 Then 'selection against AA genotype relative to BB genotype
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabV1 Then 'sorry, bad luck... you're dead, gamete B!
- Zygote_Is_Dead = 1
- End If
- End If
- If ViabV2 < 1 Then 'selection against AB genotype relative to BB genotype
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabV2 Then 'AA killed
- Zygote_Is_Dead = 1
- End If
- ElseIf ViabV2 > 1 Then 'selection against BB genotype versus AB genotype
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "B" And myRandkill > 1 / ViabV2 Then 'sorry, bad luck... you're dead, gamete B!
- Zygote_Is_Dead = 1
- End If
- End If
- If ViabV3 < 1 Then 'selection against AB genotype relative to AA genotype
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill > ViabV3 Then 'AA killed
- Zygote_Is_Dead = 1
- End If
- ElseIf ViabV3 > 1 Then 'selection against AA genotype versus AB genotype
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > 1 / ViabV3 Then 'sorry, bad luck... you're dead, gamete B!
- Zygote_Is_Dead = 1
- End If
- End If
- End If
-
- If Zygote_Is_Dead = 1 Then GoTo 100
- 'random traits
- For mytrait = 1 To NumberOfSimulatedRandomTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
- Next mytrait
-
- Next SimulatedGenotype
-
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, 0) = "SimulatedQTrait_1"
-
- 'random traits names
- For mytrait = 1 To NumberOfSimulatedRandomTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, 0) = "RandomQTrait_" & mytrait
- Next mytrait
-
- If RandomErrorRate > 0 And RandomErrorRate <= 1 Then
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For Marker = 1 To NbOfMrksInChr
- If Rnd >= 1 - RandomErrorRate Then
- If SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A" Then
- If Rnd >= (1 / 3) Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
- Else
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
- End If
- ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B" Then
- If Rnd >= (1 / 3) Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
- Else
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
- End If
- ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H" Then
- If Rnd >= 0.5 Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
- Else
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
- End If
- End If
- End If
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- Next SimulatedGenotype
- End If
- If RandomMissingDataRate > 0 And RandomMissingDataRate <= 1 Then
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For Marker = 1 To NbOfMrksInChr
- If Rnd >= 1 - RandomMissingDataRate Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "-"
- End If
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- Next SimulatedGenotype
- End If
-
-
-
-'SSD - RIL
- ElseIf SimulatedPopulationType = "SSD" Then 'it's fake but should work. however does not allow to test for biased estimates
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- MarkerPositionOld = 0
- Marker = StartRow
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "B"
- SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- myRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- myR = 2 * myRF / (1 + 2 * myRF)
- IntervalWithPreviousMarkerInRF = myR ' fake conversion of recombination rate in SSD (the 'R')
-
-' IntervalWithPreviousMarkerInR_MartinAndHospital = 1 ' fake conversion of recombination rate in SSD (the 'R')
-
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- myRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- myR = 2 * myRF / (1 + 2 * myRF)
- IntervalWithPreviousMarkerInRF = myR ' fake conversion of recombination rate in SSD (the 'R')
- End If
- 'Randomize (Rnd)
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If Genotype = "A" Then
- Genotype = "B"
- ElseIf Genotype = "B" Then
- Genotype = "A"
- End If
- End If
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
-
- 'simulate non-random trait
- If ChrQTL1 = chromosome Then
- If Marker = MarkerNumberQTL1 Then
- If Genotype = "A" Then
- myAAvalue = gauss * SD_AA_QTL1 + MeanAA_QTL1
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myAAvalue, "###.00")
- ElseIf Genotype = "B" Then
- myBBvalue = gauss * SD_BB_QTL1 + MeanBB_QTL1
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedGenotype) = Format(myBBvalue, "###.00")
- End If
- End If
- End If
- MarkerPositionOld = MarkerPosition
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
-
- For mytrait = 1 To NumberOfSimulatedRandomTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
- Next mytrait
-
- Next SimulatedGenotype
-
- If RandomErrorRate > 0 And RandomErrorRate <= 1 Then
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For Marker = 1 To NbOfMrksInChr
- If Rnd >= 1 - RandomErrorRate Then
- If SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A" Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
- ElseIf SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B" Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
- End If
- End If
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- Next SimulatedGenotype
- End If
- If RandomMissingDataRate > 0 And RandomMissingDataRate <= 1 Then
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For Marker = 1 To NbOfMrksInChr
- If Rnd >= 1 - RandomMissingDataRate Then
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "-"
- End If
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- Next SimulatedGenotype
- End If
- SimulatedGenotypes(NumberOfSimulatedMarkers + 1, 0) = "SimulatedQTrait_1"
-
- For mytrait = 1 To NumberOfSimulatedRandomTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + NumberOfSimulatedTraits + mytrait, 0) = "RandomQTrait_" & mytrait
- Next 'mytrait
-' ElseIf SimulatedPopulationType = "SSD" Then
-'
-' 'en cours a finir
-'
-' NumberOfSelfings = 6 ' Additional selfings after the F2 = S1 so 6 gives an F8
-'
-' For SimulatedGenotype = 1 To SimulatedPopulationSize
-' StartRow = 1
-' For Chromosome = 1 To NumberOfSimulatedChromosomes
-' ChrSize = VirtualMap(26 + Chromosome, 11)
-' NbOfMrksInChr = VirtualMap(26 + Chromosome, 12)
-' MarkerPositionOld = 0
-' 'Randomize (Rnd)
-' If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
-' 'Randomize (Rnd)
-' If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
-' marker = StartRow
-' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "A"
-' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "B"
-' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
-' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
-'
-' For marker = 2 To NbOfMrksInChr
-' MarkerPosition = VirtualMap(StartRow + marker + 4, 5)
-' IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
-' If MapFunctionSimul = 1 Then
-' IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
-' ElseIf MapFunctionSimul = 2 Then
-' temp = 2 * (IntervalWithPreviousMarker / 100)
-' IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
-' End If
-' 'gamete 1
-' 'Randomize (Rnd)
-' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
-' If genotype1 = "A" Then
-' genotype1 = "B"
-' ElseIf genotype1 = "B" Then
-' genotype1 = "A"
-' End If
-' End If
-' 'gamete 2
-' 'Randomize (Rnd)
-' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
-' If genotype2 = "A" Then
-' genotype2 = "B"
-' ElseIf genotype2 = "B" Then
-' genotype2 = "A"
-' End If
-' End If
-' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AA"
-' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BB"
-' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AB"
-' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BA"
-' MarkerPositionOld = MarkerPosition
-' Next marker
-'
-' StartRow = StartRow + NbOfMrksInChr
-' Next Chromosome
-'
-' For mytrait = 1 To NumberOfSimulatedRandomTraits
-' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
-' Next mytrait
-'
-' For SelfingGeneration = 1 To NumberOfSelfings
-' StartRow = 1
-'
-' For Chromosome = 1 To NumberOfSimulatedChromosomes
-' ChrSize = VirtualMap(26 + Chromosome, 11)
-' NbOfMrksInChr = VirtualMap(26 + Chromosome, 12)
-' MarkerPositionOld = 0
-'
-' If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
-'
-' If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
-' marker = StartRow
-' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "A"
-' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "B"
-' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
-' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(marker, SimulatedGenotype) = "H"
-'
-' For marker = 2 To NbOfMrksInChr
-' MarkerPosition = VirtualMap(StartRow + marker + 4, 5)
-' IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
-' If MapFunctionSimul = 1 Then
-' IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
-' ElseIf MapFunctionSimul = 2 Then
-' temp = 2 * (IntervalWithPreviousMarker / 100)
-' IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
-' End If
-' 'gamete 1
-' 'Randomize (Rnd)
-' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
-' If genotype1 = "A" Then
-' genotype1 = "B"
-' ElseIf genotype1 = "B" Then
-' genotype1 = "A"
-' End If
-' End If
-' 'gamete 2
-' 'Randomize (Rnd)
-' If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
-' If genotype2 = "A" Then
-' genotype2 = "B"
-' ElseIf genotype2 = "B" Then
-' genotype2 = "A"
-' End If
-' End If
-' If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AA"
-' If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BB"
-' If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "AB"
-' If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + marker - 1, SimulatedGenotype) = "BA"
-' MarkerPositionOld = MarkerPosition
-' Next marker
-'
-' StartRow = StartRow + NbOfMrksInChr
-' Next Chromosome
-'
-' Next SelfingGeneration
-'
-' Next SimulatedGenotype
-'
-' For mytrait = 1 To NumberOfSimulatedRandomTraits
-' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
-' Next mytrait
-
-
- End If
-
- Application.ScreenUpdating = True: DoEvents: Application.ScreenUpdating = False
-
- 'Writing results
- If NumberOfSimulatedPopulations > 1 And AutoBatchMapOn = 0 Then ' write pop in a .txt file
-
- FileSaveName = "SimulPop_" & SimulatedPopulation & ".txt"
- Open FileSaveName For Output As #1
- If SimulatedPopulationType = "BC1" Then Print #1, "data type f2 backcross"
- If SimulatedPopulationType = "F2" Then Print #1, "data type f2 intercross"
- Print #1, Format(SimulatedPopulationSize, "###"); Spc(1); Format(NumberOfSimulatedMarkers, "###"); Spc(1); "0"
- For Ligne = 1 To NumberOfSimulatedMarkers
- NomLocus = VirtualMap(Ligne + 5, 4)
- TexteLocus = ""
- For Colonne = 1 To SimulatedPopulationSize
- TexteLocus = TexteLocus & SimulatedGenotypes(Ligne, Colonne)
- Next
- Print #1, ; "*" & NomLocus; Spc(1); TexteLocus
- Next
- Close #1
-
- ElseIf AutoBatchMapOn = 1 Then ' write pop in a array
- For i = 1 To NumberOfSimulatedMarkers
- For j = 1 To SimulatedPopulationSize
- Data(j - 1, i - 1) = SimulatedGenotypes(i, j) 'stay in memory
- Next
- Next
-
- ElseIf NumberOfSimulatedPopulations = 1 And AutoBatchMapOn = 0 Then ' write pop in a sheet
- Application.StatusBar = "Writing results"
- ClearSimulatedPopulation
- OutPutSheetName = "SimulPop"
- 'MsgBox SimulatedPopulationSize
-' If MaxNumberOfColumns = 256 Then
-' If SimulatedPopulationSize <= 254 And SimulatedPopulationSize <= 508 Then
-' ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, SimulatedPopulationSize + 1) = SimulatedGenotypes
-' ElseIf SimulatedPopulationSize > 254 And SimulatedPopulationSize <= 508 Then
-' ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, 255) = SimulatedGenotypes
-' ReDim SimulatedGenotypesPlus(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, SimulatedPopulationSize - 254 + 1) As Variant
-' For i = 1 To NumberOfSimulatedMarkers
-' For j = 255 To SimulatedPopulationSize
-' SimulatedGenotypesPlus(i, j - 254) = SimulatedGenotypes(i, j)
-' Next
-' Next i
-' ThisWorkbook.Sheets("SimulPop+").Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits, SimulatedPopulationSize - 253) = SimulatedGenotypesPlus
-' End If
-' ElseIf MaxNumberOfColumns = 16384 Then
- ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedRandomTraits + 1, SimulatedPopulationSize + 1) = SimulatedGenotypes
-' End If
- Application.ScreenUpdating = False
- ThisWorkbook.Sheets("SimulMap").Activate
- Range("D6").Select
- Range(Selection, Selection.End(xlDown)).Select
- Selection.Copy
- [N22].Select
- ThisWorkbook.Sheets(OutPutSheetName).Activate
- Range("B16").Select
- Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
- :=False, Transpose:=False
- [c15].Resize(1, SimulatedPopulationSize) = genotypeNames
- Range("D4") = SimulatedPopulationType
- Range("D5") = SimulatedPopulationSize
- Range("D6") = NumberOfSimulatedMarkers
- Range("D7") = NumberOfSimulatedRandomTraits + 1
- Range("D8") = nbOfSupPops
- Range("H4") = "A"
- Range("H5") = "B"
- Range("H6") = "C"
- Range("H7") = "D"
- Range("H8") = "H"
- Range("H9") = "-"
- Range("K4") = "2"
- [b10] = "Simulated " & SimulatedPopulationType & " data " & Date & " - " & Time
- Application.CutCopyMode = False
- [K6] = ""
- [B15].Select
- End If
-Next SimulatedPopulation
-
-GoTo 1000
-900
-''Debug.Print Chromosome
-''Debug.Print StartRow
-''Debug.Print marker
-''Debug.Print SimulatedGenotype
-''Debug.Print genotype
-''Debug.Print StartRow + marker - 1
-1000
-'Application.ScreenUpdating = True
-'Next i
-
-If AutoBatchMapOn = 0 Then
- Sheets("SimulMap").[K6] = ""
- Application.StatusBar = False
-End If
-
-End Sub
-
-
-
-Public Sub Simulate_Population_From_Map_Save()
-Read_Parameters
-
-'On Error GoTo 900
-Application.ScreenUpdating = False
-If AutoBatchMapOn = 0 Then If AutoBatchMapOn = 0 Then Application.StatusBar = "Starting..."
-
-ThisWorkbook.Sheets("SimulMap").Activate
-
-'Population Parameters
-NumberOfSimulatedPopulations = [N15]
-SimulatedPopulationType = [N16] 'ONLY BC1 & F2 pops at this stage
-If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" And SimulatedPopulationType <> "BC2F1" Then MsgBox "BC1 or F2 populations only, sorry.": GoTo 1000
-SimulatedPopulationSize = [N17] 'NOT more than 508 individuals at this stage
-If AutoBatchMapOn = 0 And SimulatedPopulationSize > 508 And NumberOfSimulatedPopulations = 1 Then
- SimulatedPopulationSize = 508
- MsgBox "I can't simulate more than 508 individuals. If you need more indivuduals, please simulate 2 or more populations; this will generate Mapmaker/EXP compatible files that you can analyze using the BatchMap command."
-End If
-
-MapFunctionSimul = [N18]
-
-ChromosomeSDL1 = [R9]
-PositionSDL1 = [R10]
-ViabU = [R15] 'differential viability fA/fB for SDL1
-SDL1AbsoluteNumber = 0
-For i = 1 To ChromosomeSDL1 - 1
- SDL1AbsoluteNumber = SDL1AbsoluteNumber + Cells(26 + i, 12)
-Next
-SDL1AbsoluteNumber = SDL1AbsoluteNumber + PositionSDL1
-
-ChromosomeSDL2 = [R11]
-PositionSDL2 = [R12]
-ViabV = [R17] 'differential viability fA/fB for SDL2
-SDL2AbsoluteNumber = 0
-For i = 1 To ChromosomeSDL2 - 1
- SDL2AbsoluteNumber = SDL2AbsoluteNumber + Cells(26 + i, 12)
-Next
-SDL2AbsoluteNumber = SDL2AbsoluteNumber + PositionSDL2
-
-NumberOfSimulatedTraits = [N19]
-
-If NumberOfSimulatedPopulations > 1 Then
- If AutoBatchMapOn = 0 Then
- OperatingSystem = ThisWorkbook.Sheets("hide").Cells(8, 1)
- OperatingSystem = UCase(Left(OperatingSystem, 3))
- If OperatingSystem = "WIN" Then
- FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="Text Files (*.txt), *.txt")
- ElseIf OperatingSystem = "MAC" Then
- FileSaveName = Application.GetSaveAsFilename(Title:="Locate the folder to export the data (Don't rename the MyPop.txt file please): ", InitialFileName:="MyPop.txt", fileFilter:="TEXT")
- End If
- If FileSaveName = False Then GoTo 1000
-
- LengthOfPath = Len(FileSaveName)
- OutputPath = Left(FileSaveName, LengthOfPath - 9)
- 'MsgBox "The output folder will be " & Chr(13) & OutputPath
- End If
-End If
-
-'Reading map parameters
-If AutoBatchMapOn = 0 Then Application.StatusBar = "Reading map parameters"
-
-VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
-'TotalMapSize = [N22]
-NumberOfSimulatedMarkers = [N23]
-NumberOfSimulatedChromosomes = [R22]
-
-If NumberOfSimulatedPopulations > 1 And AutoBatchMapOn = 0 Then ' simulate genotypes and write in txt files
- For SimulatedPopulation = 1 To NumberOfSimulatedPopulations
- If AutoBatchMapOn = 0 Then Application.StatusBar = "Simulating population " & SimulatedPopulation & " of " & NumberOfSimulatedPopulations
-
- ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1, SimulatedPopulationSize + 1) As Variant
-
- StartRow = 1
-
- If SimulatedPopulationType = "BC1" Then
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- MarkerPositionOld = 0
- 'Randomize (Rnd)
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
- Marker = StartRow
- SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- 'Randomize (Rnd)
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If Genotype = "A" Then
- Genotype = "H"
- ElseIf Genotype = "H" Then
- Genotype = "A"
- End If
- End If
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- MarkerPositionOld = MarkerPosition
- Next Marker
- Next SimulatedGenotype
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
-
- ElseIf SimulatedPopulationType = "F2" Then
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- MarkerPositionOld = 0
- 'Randomize (Rnd)
- If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
- 'Randomize (Rnd)
- If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
- Marker = StartRow
- If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "A"
- If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "B"
- If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
- If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
-
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- 'gamete 1
- 'Randomize (Rnd)
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If genotype1 = "A" Then
- genotype1 = "B"
- ElseIf genotype1 = "B" Then
- genotype1 = "A"
- End If
- End If
- 'gamete 2
- 'Randomize (Rnd)
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If genotype2 = "A" Then
- genotype2 = "B"
- ElseIf genotype2 = "B" Then
- genotype2 = "A"
- End If
- End If
- If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
- If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
- If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
- If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
- MarkerPositionOld = MarkerPosition
- Next Marker
- Next SimulatedGenotype
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- End If
-
- 'Writing in .txt file
-
- FileSaveName = "SimulPop_" & SimulatedPopulation & ".txt"
- Open FileSaveName For Output As #1
- If SimulatedPopulationType = "BC1" Then Print #1, "data type f2 backcross"
- If SimulatedPopulationType = "F2" Then Print #1, "data type f2 intercross"
- Print #1, Format(SimulatedPopulationSize, "###"); Spc(1); Format(NumberOfSimulatedMarkers, "###"); Spc(1); "0"
- For Ligne = 1 To NumberOfSimulatedMarkers
- NomLocus = VirtualMap(Ligne + 5, 4)
- TexteLocus = ""
- For Colonne = 1 To SimulatedPopulationSize
- TexteLocus = TexteLocus & SimulatedGenotypes(Ligne, Colonne)
- Next
- Print #1, ; "*" & NomLocus; Spc(1); TexteLocus
- Next
- Close #1
-
- Next SimulatedPopulation
-
-ElseIf NumberOfSimulatedPopulations = 1 Or AutoBatchMapOn = 1 Then 'if only one population, write in the SimulPop sheet
- If AutoBatchMapOn = 0 Then Application.StatusBar = "Simulating population"
- ReDim SimulatedGenotypes(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize + 1) As Variant
- StartRow = 1
-
- If SimulatedPopulationType = "BC1" And ChromosomeSDL1 = 0 Then 'there is no SDL (Segregation Distortion Locus) in the genome
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- MarkerPositionOld = 0
- Marker = StartRow
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
- SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If Genotype = "A" Then
- Genotype = "H"
- ElseIf Genotype = "H" Then
- Genotype = "A"
- End If
- End If
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- MarkerPositionOld = MarkerPosition
- Next Marker
- For mytrait = 1 To NumberOfSimulatedTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
- Next mytrait
- Next SimulatedGenotype
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- For mytrait = 1 To NumberOfSimulatedTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
- Next mytrait
-
- ElseIf SimulatedPopulationType = "BC2F1" And ChromosomeSDL1 = 0 Then 'there is no SDL (Segregation Distortion Locus) in the genome
- BC2FamilySize = 4
- BC2PopulationSize = SimulatedPopulationSize * BC2FamilySize
- For SimulatedGenotype = 1 To SimulatedPopulationSize
-50
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- MarkerPositionOld = 0
- Marker = StartRow
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
- SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If Genotype = "A" Then
- Genotype = "H"
- ElseIf Genotype = "H" Then
- Genotype = "A"
- End If
- End If
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- MarkerPositionOld = MarkerPosition
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
-' For mytrait = 1 To NumberOfSimulatedTraits
-' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
-' Next mytrait
- Next SimulatedGenotype
-' For mytrait = 1 To NumberOfSimulatedTraits
-' SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
-' Next mytrait
-
- ElseIf SimulatedPopulationType = "BC1" And ChromosomeSDL1 > 0 Then 'there is a SDL (Segregation Distortion Locus) in the genome
- ''Debug.Print "zzz"
- For SimulatedGenotype = 1 To SimulatedPopulationSize
-100
- StartRow = 1
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- MarkerPositionOld = 0
- Marker = StartRow
- If Rnd > 0.5 Then Genotype = "A" Else Genotype = "H"
- SimulatedGenotypes(Marker, SimulatedGenotype) = Genotype
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If Genotype = "A" Then
- Genotype = "H"
- ElseIf Genotype = "H" Then
- Genotype = "A"
- End If
- End If
- SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = Genotype
- MarkerPositionOld = MarkerPosition
- Next Marker
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
-
- 'fA/fH = u
- 'frequency of A = fA = u /(1+u)
- 'frequency of B = fB = 1 /(1+u)
- myRandkill = Rnd
- If ViabU < 1 Then 'selection against AA genotypes or A gametes
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > (ViabU / (1 + ViabU)) Then 'sorry, bad luck... you're dead, gamete A!
- 'kill individual/gamete and simulate again
- GoTo 100
- End If
- ElseIf ViabU > 1 Then 'selection against H genotypes or B gametes
- If SimulatedGenotypes(SDL1AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill < (1 / (1 + ViabU)) Then 'sorry, bad luck... you're dead, gamete B!
- 'kill individual/gamete and simulate again
- GoTo 100
- End If
- End If
- If ChromosomeSDL2 > 0 Then
- If ViabV < 1 Then 'selection against AA genotypes or A gametes
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "A" And myRandkill > (ViabV / (1 + ViabV)) Then 'sorry, bad luck... you're dead, gamete A!
- 'kill individual/gamete and simulate again
- GoTo 100
- End If
- ElseIf ViabV > 1 Then 'selection against H genotypes or B gametes
- If SimulatedGenotypes(SDL2AbsoluteNumber, SimulatedGenotype) = "H" And myRandkill < (1 / (1 + ViabV)) Then 'sorry, bad luck... you're dead, gamete B!
- 'kill individual/gamete and simulate again
- GoTo 100
- End If
- End If
- End If
- For mytrait = 1 To NumberOfSimulatedTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
- Next mytrait
- Next SimulatedGenotype
- For mytrait = 1 To NumberOfSimulatedTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
- Next mytrait
-
- ElseIf SimulatedPopulationType = "F2" Then
- For chromosome = 1 To NumberOfSimulatedChromosomes
- ChrSize = VirtualMap(26 + chromosome, 11)
- NbOfMrksInChr = VirtualMap(26 + chromosome, 12)
- For SimulatedGenotype = 1 To SimulatedPopulationSize
- MarkerPositionOld = 0
- 'Randomize (Rnd)
- If Rnd > 0.5 Then genotype1 = "A" Else genotype1 = "B"
- 'Randomize (Rnd)
- If Rnd > 0.5 Then genotype2 = "B" Else genotype2 = "A"
- Marker = StartRow
- If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "A"
- If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "B"
- If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
- If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(Marker, SimulatedGenotype) = "H"
-
- For Marker = 2 To NbOfMrksInChr
- MarkerPosition = VirtualMap(StartRow + Marker + 4, 5)
- IntervalWithPreviousMarker = MarkerPosition - MarkerPositionOld
- If MapFunctionSimul = 1 Then
- IntervalWithPreviousMarkerInRF = 0.5 * (1 - Exp(-2 * (IntervalWithPreviousMarker / 100))) ' Haldane inverse function
- ElseIf MapFunctionSimul = 2 Then
- temp = 2 * (IntervalWithPreviousMarker / 100)
- IntervalWithPreviousMarkerInRF = 0.5 * ((Exp(temp) - Exp(-temp)) / (Exp(temp) + Exp(-temp))) 'Kosambi inverse funciton
- End If
- 'gamete 1
- 'Randomize (Rnd)
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If genotype1 = "A" Then
- genotype1 = "B"
- ElseIf genotype1 = "B" Then
- genotype1 = "A"
- End If
- End If
- 'gamete 2
- 'Randomize (Rnd)
- If Rnd > 1 - IntervalWithPreviousMarkerInRF Then 'a recombination occurred
- If genotype2 = "A" Then
- genotype2 = "B"
- ElseIf genotype2 = "B" Then
- genotype2 = "A"
- End If
- End If
- If genotype1 = "A" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "A"
- If genotype1 = "B" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "B"
- If genotype1 = "A" And genotype2 = "B" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
- If genotype1 = "B" And genotype2 = "A" Then SimulatedGenotypes(StartRow + Marker - 1, SimulatedGenotype) = "H"
- MarkerPositionOld = MarkerPosition
- Next Marker
- Next SimulatedGenotype
- For mytrait = 1 To NumberOfSimulatedTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, SimulatedGenotype) = Format(100 + Rnd * 20, "###.00")
- Next mytrait
- StartRow = StartRow + NbOfMrksInChr
- Next chromosome
- For mytrait = 1 To NumberOfSimulatedTraits
- SimulatedGenotypes(NumberOfSimulatedMarkers + mytrait, 0) = "RandomQTrait_" & mytrait
- Next mytrait
- End If
-
- If AutoBatchMapOn = 0 Then
- Application.StatusBar = "Writing results"
- ClearSimulatedPopulation
- OutPutSheetName = "SimulPop"
- 'MsgBox SimulatedPopulationSize
- If SimulatedPopulationSize <= 254 And SimulatedPopulationSize <= 508 Then
- ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize + 1) = SimulatedGenotypes
- ElseIf SimulatedPopulationSize > 254 And SimulatedPopulationSize <= 508 Then
- ThisWorkbook.Sheets(OutPutSheetName).Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, 255) = SimulatedGenotypes
- ReDim SimulatedGenotypesPlus(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize - 254 + 1) As Variant
- For i = 1 To NumberOfSimulatedMarkers
- For j = 255 To SimulatedPopulationSize
- SimulatedGenotypesPlus(i, j - 254) = SimulatedGenotypes(i, j)
- Next
- Next i
- ThisWorkbook.Sheets("SimulPop+").Range("B15").Resize(NumberOfSimulatedMarkers + 1 + NumberOfSimulatedTraits, SimulatedPopulationSize - 253) = SimulatedGenotypesPlus
- End If
- Application.ScreenUpdating = False
- ThisWorkbook.Sheets("SimulMap").Activate
- Range("D6").Select
- Range(Selection, Selection.End(xlDown)).Select
- Selection.Copy
- [N22].Select
- ThisWorkbook.Sheets(OutPutSheetName).Activate
- Range("B16").Select
- Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
- :=False, Transpose:=False
-
- Range("D4") = SimulatedPopulationType
- Range("D5") = SimulatedPopulationSize
- Range("D6") = NumberOfSimulatedMarkers
- Range("D7") = NumberOfSimulatedTraits
- Range("H4") = "A"
- Range("H5") = "B"
- Range("H6") = "C"
- Range("H7") = "D"
- Range("H8") = "H"
- Range("H9") = "-"
- Range("K4") = "2"
- If SimulatedPopulationType = "BC1" Then
- [b10] = "Simulated BC1 data " & Date & " - " & Time
- ElseIf SimulatedPopulationType = "F2" Then
- [b10] = "Simulated F2 data " & Date & " - " & Time
- End If
- Application.CutCopyMode = False
- [B15].Select
- ElseIf AutoBatchMapOn = 1 Then
-' MsgBox SimulatedPopulationSize
- For i = 1 To NumberOfSimulatedMarkers
- For j = 1 To SimulatedPopulationSize
- Data(j - 1, i - 1) = SimulatedGenotypes(i, j) 'stay in memory
- Next
- Next
- OutPutSheetName = "Data"
-
- ThisWorkbook.Sheets(OutPutSheetName).Range("D4") = SimulatedPopulationType
- ThisWorkbook.Sheets(OutPutSheetName).Range("D5") = SimulatedPopulationSize
- ThisWorkbook.Sheets(OutPutSheetName).Range("D6") = NumberOfSimulatedMarkers
- ThisWorkbook.Sheets(OutPutSheetName).Range("D7") = "0"
- ThisWorkbook.Sheets(OutPutSheetName).Range("H4") = "A"
- ThisWorkbook.Sheets(OutPutSheetName).Range("H5") = "B"
- ThisWorkbook.Sheets(OutPutSheetName).Range("H6") = "C"
- ThisWorkbook.Sheets(OutPutSheetName).Range("H7") = "D"
- ThisWorkbook.Sheets(OutPutSheetName).Range("H8") = "H"
- ThisWorkbook.Sheets(OutPutSheetName).Range("H9") = "-"
- ThisWorkbook.Sheets(OutPutSheetName).Range("K4") = "2"
- End If
-
-End If
-
-GoTo 1000
-900
-''Debug.Print Chromosome
-''Debug.Print StartRow
-''Debug.Print marker
-''Debug.Print SimulatedGenotype
-''Debug.Print genotype
-''Debug.Print StartRow + marker - 1
-1000
-'Application.ScreenUpdating = True
-'Next i
-If AutoBatchMapOn = 0 Then Application.StatusBar = False
-End Sub
-
-Public Sub ClearSimulatedPopulation()
- Application.ScreenUpdating = False
- ThisWorkbook.Sheets("SimulPop").Activate
- Range("B15:xfd1048576").ClearContents
- Range("D4").ClearContents
- Range("D5").ClearContents
- Range("D6").ClearContents
- Range("D7").ClearContents
- Range("H4").ClearContents
- Range("H5").ClearContents
- Range("H6").ClearContents
- Range("H7").ClearContents
- Range("H8").ClearContents
- Range("H9").ClearContents
- Range("K4").ClearContents
- [b10].ClearContents
-' ThisWorkbook.Sheets("SimulPop+").Activate
-' Range("B15:IV60000").ClearContents
-' Range("D4").ClearContents
-' Range("D5").ClearContents
-' Range("D6").ClearContents
-' Range("D7").ClearContents
-' Range("H4").ClearContents
-' Range("H5").ClearContents
-' Range("H6").ClearContents
-' Range("H7").ClearContents
-' Range("H8").ClearContents
-' Range("H9").ClearContents
-' Range("K4").ClearContents
-' [B13].ClearContents
- ThisWorkbook.Sheets("SimulPop").Activate
-If AutoBatchMapOn = 0 And ClearAllResultsMode = 0 Then Application.ScreenUpdating = True
-End Sub
-
-
-Public Sub Clear_BatchMap_Results()
-Application.ScreenUpdating = False
-If ThisWorkbook.Sheets("BatchMap").[h8] <> "" Then
- If ClearAllResultsMode = 0 Then
- msg = "Are you sure you want to clear the batch results?"
- Style = vbYesNo + vbCritical + vbDefaultButton1
- Title = "Clear results"
- Ctxt = 1000
- response = MsgBox(msg, Style, Title)
- End If
-
- If response = vbYes Or ClearAllResultsMode = 1 Then
- If MaxNumberOfColumns = 256 Then
- ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
- ThisWorkbook.Sheets("BatchMap").Range("H5:IV6").Interior.ColorIndex = xlNone
- Else
- ThisWorkbook.Sheets("BatchMap").Range("A5:XFD60000").ClearContents
- ThisWorkbook.Sheets("BatchMap").Range("H5:XFD6").Interior.ColorIndex = xlNone
- End If
- ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
- ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
- ThisWorkbook.Sheets("BatchMap").Range("C8:G60000").Interior.ColorIndex = xlNone
-
- Else
- GoTo 1000
- End If
-End If
-'[H8].Select
-1000
-'If AutoBatchMapOn = 0 And ClearAllResultsMode = 0 Then Application.ScreenUpdating = True
-End Sub
-
-Public Sub Clear_BigBatchMap_Results()
-Application.ScreenUpdating = False
-If [c6] <> "" Then
- If ClearAllResultsMode = 0 Then
- msg = "Are you sure you want to clear the batch results?"
- Style = vbYesNo + vbCritical + vbDefaultButton1
- Title = "Clear results"
- Ctxt = 1000
- response = MsgBox(msg, Style, Title)
- End If
- If response = vbYes Or ClearAllResultsMode = 1 Then
- If MaxNumberOfColumns = 256 Then
- ThisWorkbook.Sheets("BigBatch").Range("A4:IV60000").ClearContents
- Else
- ThisWorkbook.Sheets("BigBatch").Range("A4:XFD60000").ClearContents
- End If
- Else
- GoTo 1000
- End If
-End If
-[c6].Select
-1000
-If AutoBatchMapOn = 0 And ClearAllResultsMode = 0 Then Application.ScreenUpdating = True
-End Sub
-
-Public Sub Compute_Stats_Batch()
-'On Error GoTo 900
-Application.ScreenUpdating = False
-Application.StatusBar = "Computing statistics..."
-
-ThisWorkbook.Sheets("BatchMap").Activate
-'Expected cM values from simulated map
-NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
-For i = 2 To NumberOfMarkers
- ExpectedRelativeDistance = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 5) - ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 5)
- ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6) = ExpectedRelativeDistance
- If ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 2) <> ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2) Then 'new chr is detected
- ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6).ClearContents
- End If
-Next i
-
-NumberOfProcessedFiles = [D4]
-'Average etc on batch results
-For i = 1 To NumberOfMarkers
- mkchr = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2)
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 1) = mkchr
- SumOfDistances = 0
- MinDist = 1000000
- MaxDist = 0
- ExpectedRelativeDistance = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
- If ExpectedRelativeDistance <> "" Then
- For SimPop = 1 To NumberOfProcessedFiles
- BatchDist = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
- SumOfDistances = SumOfDistances + BatchDist
- If BatchDist < MinDist Then MinDist = BatchDist
- If BatchDist > MaxDist Then MaxDist = BatchDist
- Next
- AverageDistance = SumOfDistances / NumberOfProcessedFiles
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 3) = MinDist
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 4) = MaxDist
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 5) = AverageDistance
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = AverageDistance - ExpectedRelativeDistance
- End If
-Next i
-
-For SimPop = 1 To NumberOfProcessedFiles
- TotalMapSize = 0
- For i = 1 To NumberOfMarkers
- BatchDist = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
- If BatchDist <> "" Then
- TotalMapSize = TotalMapSize + BatchDist
- End If
- Next
- ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7) = TotalMapSize
- ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7) = TotalMapSize / NumberOfMarkers 'mk density
-Next
-
-SumAverageSize = 0
-SumAverageDensity = 0
-MinSize = 1000000
-MaxSize = 0
-MinDensity = 1000000
-MaxDensity = 0
-
-For SimPop = 1 To NumberOfProcessedFiles
- Mapsize = ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7)
- mapdensity = ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7)
- If Mapsize > MaxSize Then MaxSize = Mapsize
- If Mapsize < MinSize Then MinSize = Mapsize
- If mapdensity > MaxDensity Then MaxDensity = mapdensity
- If mapdensity < MinDensity Then MinDensity = mapdensity
- SumAverageSize = SumAverageSize + Mapsize
- SumAverageDensity = SumAverageDensity + mapdensity
-Next
-AverageSize = SumAverageSize / NumberOfProcessedFiles
-AverageDensity = SumAverageDensity / NumberOfProcessedFiles
-
-[C5] = MinSize
-[D5] = MaxSize
-[c6] = MinDensity
-[D6] = MaxDensity
-[E5] = AverageSize
-[E6] = AverageDensity
-
-[G5] = "Total map size"
-[G6] = "Marker density"
-[A7] = "Chr"
-[b7] = "Marker"
-[C7] = "Min"
-[D7] = "Max"
-[E7] = "Average"
-[F7] = "Expected"
-[G7] = "Diff."
-
-Range(Cells(8, 3), Cells(7 + NumberOfMarkers, 7)).Select
-Selection.Interior.ColorIndex = 15
-Range(Cells(5, 8), Cells(6, 256)).Select
-Selection.Interior.ColorIndex = 15
-
-GoTo 1000
-900
-MsgBox "An error occurred."
-1000
-[h8].Select
-Application.StatusBar = False
-'Application.ScreenUpdating = True
-End Sub
-
-Public Sub Compute_Stats_Batch_Chi2()
-'On Error GoTo 900
-Application.ScreenUpdating = False
-Application.StatusBar = "Computing statistics..."
-
-ThisWorkbook.Sheets("BatchMap").Activate
-'Expected cM values from simulated map
-NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
-For i = 2 To NumberOfMarkers
- ExpectedRelativeDistance = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 5) - ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 5)
- 'keep it or it won't work
- 'ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6) = ExpectedRelativeDistance
- If ThisWorkbook.Sheets("SimulMap").Cells(i + 4, 2) <> ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2) Then 'new chr is detected
- ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 6).ClearContents
- End If
-Next i
-
-NumberOfProcessedFiles = ThisWorkbook.Sheets("BatchMap").[D4]
-
-MyBatchresults = ThisWorkbook.Sheets("BatchMap").Range(Cells(1, 1), Cells(NumberOfMarkers + 7, NumberOfProcessedFiles + 7)).Value
-
-'Average etc on batch results
-For i = 1 To NumberOfMarkers
- mkchr = ThisWorkbook.Sheets("SimulMap").Cells(i + 5, 2)
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 1) = mkchr
- SumOfChi2 = 0
- MinChi2 = 1000000
- MaxChi2 = 0
- 'ExpectedRelativeDistance = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
- If ExpectedRelativeDistance <> "" Then
- For SimPop = 1 To NumberOfProcessedFiles
- BatchChi2 = MyBatchresults(i + 7, SimPop + 7)
- SumOfChi2 = SumOfChi2 + BatchChi2
- If BatchChi2 < MinChi2 Then MinChi2 = BatchChi2
- If BatchChi2 > MaxChi2 Then MaxChi2 = BatchChi2
- Next
- AverageChi2 = SumOfChi2 / NumberOfProcessedFiles
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 3) = MinChi2
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 4) = MaxChi2
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 5) = AverageChi2
- End If
-Next i
-
-'ranks
-SDL1on = ThisWorkbook.Sheets("SimulMap").[R9]
-SDL2on = ThisWorkbook.Sheets("SimulMap").[R11]
-If SDL1on = 1 Then SDL1number = ThisWorkbook.Sheets("SimulMap").[R10]
-If SDL2on = 1 Then SDL2number = ThisWorkbook.Sheets("SimulMap").[R12]
-'For i = 2 To NumberOfMarkers - 1
-' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) = 0
-' 'ExpectedRelativeDistance = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
-' For SimPop = 1 To NumberOfProcessedFiles
-' BatchChi2 = MyBatchresults(i + 7, SimPop + 7)
-' BatchChi2Before = MyBatchresults(i + 6, SimPop + 7)
-' BatchChi2After = MyBatchresults(i + 8, SimPop + 7)
-' If BatchChi2 < BatchChi2Before Or BatchChi2 < BatchChi2After Then
-' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) + 1
-' If i = SDL1number Or i = SDL2number Then
-' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7).Select
-' Selection.Interior.ColorIndex = 15
-' End If
-' End If
-'' If BatchChi2 < BatchChi2Before Then
-'' If i = SDL1number Or i = SDL2number Then
-'' ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) = ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) + 1
-'' ThisWorkbook.Sheets("BatchMap").Cells(i + 6, SimPop + 7).Select
-'' Selection.Interior.ColorIndex = 15
-'' End If
-'' End If
-'' If BatchChi2 < BatchChi2After Then
-'' If i = SDL1number Or i = SDL2number Then
-'' ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) = ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) + 1
-'' ThisWorkbook.Sheets("BatchMap").Cells(i + 8, SimPop + 7).Select
-'' Selection.Interior.ColorIndex = 15
-'' End If
-'' End If
-' Next
-' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6) / NumberOfProcessedFiles)
-' ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = 100 - ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 6)
-'' If i = SDL1number Or i = SDL2number Then
-''' ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 6, 7) / NumberOfProcessedFiles)
-''' ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 8, 7) / NumberOfProcessedFiles)
-'' End If
-'Next i
-
-
-For SimPop = 1 To NumberOfProcessedFiles
- SDL1isNotaPeak = 0
- mychi2SDL1 = ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, SimPop + 7)
- For i = 1 To NumberOfMarkers
- myChi2 = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
- If myChi2 > mychi2SDL1 Then
- 'it's a peak, not on SDL1
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) + 1
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7).Select
- Selection.Interior.ColorIndex = 15
- SDL1isNotaPeak = 1
- End If
- Next
- If SDL1isNotaPeak = 1 Then 'in this pop
- 'SDL1 is not a peak
- ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) = ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) + 1
- End If
-Next
-
-For i = 1 To NumberOfMarkers
- ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(i + 7, 7)) / NumberOfProcessedFiles
-Next
-
-ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) = 100 * (ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6) / NumberOfProcessedFiles)
-ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 7) = 100 - ThisWorkbook.Sheets("BatchMap").Cells(SDL1number + 7, 6)
-
-'For SimPop = 1 To NumberOfProcessedFiles
-' TotalMapSize = 0
-' For i = 1 To NumberOfMarkers
-' BatchDist = ThisWorkbook.Sheets("BatchMap").Cells(i + 7, SimPop + 7)
-' If BatchDist <> "" Then
-' TotalMapSize = TotalMapSize + BatchDist
-' End If
-' Next
-' ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7) = TotalMapSize
-' ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7) = TotalMapSize / NumberOfMarkers 'mk density
-'Next
-
-SumAverageChi2 = 0
-SumAverageDensity = 0
-MinChi2 = 1000000
-MaxChi2 = 0
-MinDensity = 1000000
-MaxDensity = 0
-
-For SimPop = 1 To NumberOfProcessedFiles
- MapChi2 = ThisWorkbook.Sheets("BatchMap").Cells(5, SimPop + 7)
- mapdensity = ThisWorkbook.Sheets("BatchMap").Cells(6, SimPop + 7)
- If MapChi2 > MaxChi2 Then MaxChi2 = MapChi2
- If MapChi2 < MinChi2 Then MinChi2 = MapChi2
- If mapdensity > MaxDensity Then MaxDensity = mapdensity
- If mapdensity < MinDensity Then MinDensity = mapdensity
- SumAverageChi2 = SumAverageChi2 + MapChi2
- SumAverageDensity = SumAverageDensity + mapdensity
-Next
-AverageChi2 = SumAverageChi2 / NumberOfProcessedFiles
-AverageDensity = SumAverageDensity / NumberOfProcessedFiles
-
-[C5] = MinChi2
-[D5] = MaxChi2
-[c6] = MinDensity
-[D6] = MaxDensity
-[E5] = AverageChi2
-[E6] = AverageDensity
-
-'[G5] = "Total map size"
-'[G6] = "Marker density"
-[A7] = "Chr"
-[b7] = "Marker"
-[C7] = "Min"
-[D7] = "Max"
-[E7] = "Average"
-[F7] = "% no peak"
-[G7] = "% peak"
-
-Range(Cells(8, 3), Cells(7 + NumberOfMarkers, 7)).Select
-Selection.Interior.ColorIndex = 15
-Range(Cells(5, 8), Cells(6, 256)).Select
-Selection.Interior.ColorIndex = 15
-
-GoTo 1000
-900
-MsgBox "An error occurred."
-1000
-[h8].Select
-Application.StatusBar = False
-'Application.ScreenUpdating = True
-End Sub
-
-Public Sub ShowDistribMapSizesFromBigBatch()
- FromBigBatch = 1
- ShowDistributionMapSizes
- FromBigBatch = 0
-End Sub
-
-Public Sub ShowDistributionMapSizes()
-
-Application.ScreenUpdating = False
-Application.StatusBar = "cleaning..."
-ThisWorkbook.Sheets("Distrib").Activate
-
-NumberOfIntervals = ThisWorkbook.Sheets("Distrib").[M516]
-ThisWorkbook.Sheets("Distrib").Cells.ClearContents
-ThisWorkbook.Sheets("Distrib").Cells.Interior.ColorIndex = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlDiagonalDown).LineStyle = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlDiagonalUp).LineStyle = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeLeft).LineStyle = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeTop).LineStyle = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeBottom).LineStyle = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlEdgeRight).LineStyle = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlInsideVertical).LineStyle = xlNone
- ThisWorkbook.Sheets("Distrib").Cells.Borders(xlInsideHorizontal).LineStyle = xlNone
-
-popType = ThisWorkbook.Sheets("SimulMap").[N16]
-popsize = ThisWorkbook.Sheets("SimulMap").[N17]
-EmapSize = ThisWorkbook.Sheets("SimulMap").[N22]
-
-If FromBigBatch = 0 Then
- MyBatchMatrix = ThisWorkbook.Sheets("BatchMap").Range("A5:IV6").Value
- valeurMax = ThisWorkbook.Sheets("BatchMap").[D5]
- valeurMin = ThisWorkbook.Sheets("BatchMap").[C5]
- NumberOfValues = ThisWorkbook.Sheets("BatchMap").[D4]
-Else
- MyBatchMatrix = ThisWorkbook.Sheets("BigBatch").Range("C6:D10010").Value
-
- ThisWorkbook.Sheets("BigBatch").Activate
- NumberOfValues = ThisWorkbook.Sheets("SimulMap").[n3]
- '
- Range("C6:D10005").Select
- Range("D6").Activate
- Selection.Sort Key1:=Range("D6"), Order1:=xlAscending, Header:=xlGuess, _
- OrderCustom:=1, MatchCase:=False, Orientation:=xlTopToBottom
-
- [D6].Select
- valeurMin = [D6]
- valeurMax = Cells(5 + NumberOfValues, 4)
-End If
-
-Application.StatusBar = "writing intervals"
-If NumberOfIntervals = 0 Or NumberOfIntervals = "" Then NumberOfIntervals = 40
-[M516] = NumberOfIntervals
-IntervalSize = Int(valeurMax - valeurMin) / NumberOfIntervals
-
-ReDim VectorFrequencies(1, NumberOfIntervals + 1) As Long
-ReDim VectorBounds(2, NumberOfIntervals + 16) As Double
-
-mininterval = valeurMin
-For Interval = 1 To NumberOfIntervals + 1
- ThisWorkbook.Sheets("Distrib").Cells(510, Interval + 15) = mininterval
- VectorBounds(0, Interval + 15) = mininterval
- maxinterval = mininterval + IntervalSize
- ThisWorkbook.Sheets("Distrib").Cells(509, Interval + 15) = maxinterval
- VectorBounds(1, Interval + 15) = maxinterval
- mininterval = maxinterval
- 'ThisWorkbook.Sheets("Distrib").Cells(515, interval + 15) = "0"
- VectorFrequencies(0, Interval - 1) = 0
-Next
-
-Application.StatusBar = "counting frequencies"
-For Colonne = 8 To NumberOfValues + 7
- If FromBigBatch = 0 Then Mapsize = MyBatchMatrix(1, Colonne) Else Mapsize = MyBatchMatrix(Colonne - 7, 2)
- 'ThisWorkbook.Sheets("Distrib").Cells(5, Colonne) = MapSize
- For Interval = 1 To NumberOfIntervals + 1
-' If MapSize >= ThisWorkbook.Sheets("Distrib").Cells(510, interval + 15) Then
-' If MapSize < ThisWorkbook.Sheets("Distrib").Cells(509, interval + 15) Then
-' VectorFrequencies(0, interval + 15) = VectorFrequencies(0, interval + 15) + 1
-' ThisWorkbook.Sheets("Distrib").Cells(515, interval + 15) = ThisWorkbook.Sheets("Distrib").Cells(515, interval + 15) + 1
-' End If
-' End If
- If Mapsize >= VectorBounds(0, Interval + 15) Then
- If Mapsize < VectorBounds(1, Interval + 15) Then
- VectorFrequencies(0, Interval - 1) = VectorFrequencies(0, Interval - 1) + 1
- End If
- End If
- Next
-Next
-
-[P515].Resize(1, NumberOfIntervals + 1) = VectorFrequencies
-
-Application.StatusBar = "drawing..."
-For Interval = 1 To NumberOfIntervals + 1
- effectif = VectorFrequencies(0, Interval - 1)
- For Ligne = 1 To effectif
- ThisWorkbook.Sheets("Distrib").Cells(500 - Ligne, Interval + 15).Interior.ColorIndex = 25
- Next Ligne
-Next
-Application.StatusBar = "finishing..."
-
-ThisWorkbook.Sheets("Distrib").Activate
-If FromBigBatch = 0 Then
- [M517].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.005)": [K517] = "Percent. 0.005"
- [M518].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.995)": [K518] = "Percent. 0.995"
- [M519].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.025)": [K519] = "Percent. 0.025"
- [M520].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.975)": [K520] = "Percent. 0.975"
- [M521].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.05)": [K521] = "Percent. 0.05"
- [M522].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.95)": [K522] = "Percent. 0.95"
- [M523].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.1666)": [K523] = "Percent. 0.167"
- [M524].Formula = "=PERCENTILE(BatchMap!H5:IV5,0.8333)": [K524] = "Percent. 0.833"
- [M525].Formula = "=MEDIAN(BatchMap!H5:IV5,0.8333)": [K525] = "Median"
- [M526].Formula = "=Average(BatchMap!H5:IV5)": [K526] = "Average"
-
- ActiveSheet.Shapes("cbDrawAgain").Select
- Selection.OnAction = "ShowDistributionMapSizes"
-
- ActiveSheet.Shapes("cbBack").Select
- Selection.OnAction = "ActiverBatchMap"
-Else
-
- [M517].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.005)": [K517] = "Percent. 0.005"
- [M518].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.995)": [K518] = "Percent. 0.995"
- [M519].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.025)": [K519] = "Percent. 0.025"
- [M520].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.975)": [K520] = "Percent. 0.975"
- [M521].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.05)": [K521] = "Percent. 0.05"
- [M522].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.95)": [K522] = "Percent. 0.95"
- [M523].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.1666)": [K523] = "Percent. 0.167"
- [M524].Formula = "=PERCENTILE(BigBatch!D6:D60000,0.8333)": [K524] = "Percent. 0.833"
- [M525].Formula = "=MEDIAN(BigBatch!D6:D60000,0.5)": [K525] = "Median"
- [M526].Formula = "=Average(BigBatch!D6:D60000)": [K526] = "Average"
-
- ActiveSheet.Shapes("cbDrawAgain").Select
- Selection.OnAction = "ShowDistribMapSizesFromBigBatch"
-
- ActiveSheet.Shapes("cbBack").Select
- Selection.OnAction = "ActiverBigBatchMap"
-
-End If
-
-[M516] = NumberOfIntervals
-[o516] = "Histogram of map sizes"
-[K516] = "Number of intervals:"
-[o518] = "Based on [P1 x P2] simulated map "
-[o519] = NumberOfValues & " " & popType & " populations of " & popsize & " individuals simulated"
-[o520] = "Expected map size: " & Format(EmapSize, "####.##") & " cM"
-
-1000
-[M516].Select
-Application.StatusBar = False
-
-End Sub
-
-
-Public Sub Draw_Simulated_Map()
-Application.StatusBar = "Starting"
-Application.ScreenUpdating = False
-Dim MyTime
-MyTime = Time
-
-'Init
-'If Probleme = 1 Then GoTo 1000
-
-' Sort_Frameed_Map Macro
-ThisWorkbook.Sheets("SimulMap").Activate
-
-If [b6] = "" Then MsgBox "No simulated map to draw": GoTo 1000
-
-'remise ö z_ro de la feuille de r_sultats ("Draw")
-Application.DisplayAlerts = False
- ThisWorkbook.Sheets("DrawSimulMap").Delete
- ThisWorkbook.Sheets("DrawSimulMap0").Select
- ThisWorkbook.Sheets("DrawSimulMap0").Copy Before:=ThisWorkbook.Sheets(11)
- ThisWorkbook.Sheets("DrawSimulMap0 (2)").Select
- ThisWorkbook.Sheets("DrawSimulMap0 (2)").Name = "DrawSimulMap"
- ThisWorkbook.Sheets("DrawSimulMap0").Activate
-Application.DisplayAlerts = True
-
-ResultSheetName = "DrawSimulMap"
-
-ThisWorkbook.Sheets("SimulMap").Activate
-ThisWorkbook.Sheets("SimulMap").Range("B6", Range("B1048576").End(xlUp)).Select
-NbOfRowsMap = Selection.Rows.Count
-[b6].Select
-
-TotalNumberOfMarkers = NbOfRowsMap
-
-firstRow = 6
-LastRow = firstRow + TotalNumberOfMarkers - 1
-
-Read_Map_Drawing_Parameters
-MyMinLabelsSpacing = MyLabelsSpacing
-
-If EchelleVert = "" Or EchelleVert = 0 Then EchelleVert = Application.InputBox(prompt:="Drawing scale? (Suggestion: choose from 1 to 5)", Title:="Draw Map", Type:=1)
-If EchelleVert = False Then GoTo 1000
-Application.StatusBar = "Resetting window"
-
-Application.StatusBar = "Loading data"
-'VirtualRawData = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
-VirtualRawData = ThisWorkbook.Sheets("SimulMap").Range(Cells(1, 1), Cells(firstRow + TotalNumberOfMarkers, 26)).Value
-ThisWorkbook.Sheets(ResultSheetName).Activate
-
-ChrSpace = MyChromosomeSpacing * 15
-SizeSmallSecondLine = EchelleHorizont
-LargCarte = 7
-
-Xorigin = 0
-Yorigin = 100
-
-MarkerChromosomeOld = 0
-FirstChromosome = ThisWorkbook.Sheets("DrawSimulMap").[b6]
-
-Application.StatusBar = "Drawing map..."
-
-For Row = firstRow To LastRow
- MarkerChromosome = VirtualRawData(Row, 2)
- If MarkerChromosome <> MarkerChromosomeOld Then ' new LG
- Application.StatusBar = "Drawing LG " & MarkerChromosome
-
- For Row2 = Row To TotalNumberOfMarkers + firstRow 'look for chr size
- If VirtualRawData(Row2, 2) <> MarkerChromosome Then
- ChromosomeSize = VirtualRawData(Row2 - 1, 5)
- NbOfMarkersInChr = Row2 - Row
- GoTo 100
- End If
- Next Row2
-100
- If LabelPositionsOption = 2 Then
- MarkerLabelPositionOld = 0 - Yorigin
- ElseIf LabelPositionsOption = 1 Then 'even mark label positions
- MyLabelsSpacing = ChromosomeSize * EchelleVert / (NbOfMarkersInChr - 1)
- If MyMinLabelsSpacing < MyLabelsSpacing Then MyLabelsSpacing = MyMinLabelsSpacing
- MarkerLabelPositionOld = 0 - MyLabelsSpacing / EchelleVert
- End If
-
- With ActiveSheet.Shapes.AddLine(Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, _
- Yorigin + 5, _
- Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, _
- Yorigin + ChromosomeSize * EchelleVert + 5)
- .Name = "MarkChr_" & MarkerChromosome
- End With
- With ActiveSheet.Shapes.AddShape(msoShapeRectangle, Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, Yorigin - 20, 100#, MyFontSize + 10)
- .TextFrame.Characters.Text = "LG " & MarkerChromosome
- .Fill.Visible = False
- .Line.Visible = False
- .Name = "MarkChrName_" & MarkerChromosome
- .TextFrame.Characters.Font.Name = MyFontName
- .TextFrame.Characters.Font.Size = MyFontSize + 5
- End With
- MarkerChromosomeOld = MarkerChromosome
- End If
-
- MarkerName = VirtualRawData(Row, 4)
- MarkerPosition = VirtualRawData(Row, 5) ' absolute positions
-
- If LabelPositionsOption = 2 Then
- If MarkerPosition - MarkerLabelPositionOld < MyLabelsSpacing / EchelleVert Then 'if < 5 cm
- MarkerLabelPosition = MarkerLabelPositionOld + MyLabelsSpacing / EchelleVert
- MarkerLabelPositionOld = MarkerLabelPosition
- Else
- MarkerLabelPosition = MarkerPosition
- MarkerLabelPositionOld = MarkerLabelPosition
- End If
- ElseIf LabelPositionsOption = 1 Then
- If MarkerPosition - MarkerLabelPositionOld > MyLabelsSpacing Then
- MarkerLabelPositionOld = MarkerLabelPositionOld + (MarkerPosition - MarkerLabelPositionOld) / 1.5
- End If
- MarkerLabelPosition = MarkerLabelPositionOld + MyLabelsSpacing / EchelleVert
- MarkerLabelPositionOld = MarkerLabelPosition
- End If
- MarkerNumber = Row
-
- With ActiveSheet.Shapes.AddLine(Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 16, Yorigin + MarkerPosition * EchelleVert + 5, Xorigin + _
- (MarkerChromosome - FirstChromosome) * ChrSpace - 9, Yorigin + MarkerPosition * EchelleVert + 5)
- '.Name = "Markline_" & MarkerNumber
- End With
- With ActiveSheet.Shapes.AddLine(Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 9, _
- Yorigin + MarkerPosition * EchelleVert + 5, _
- Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace - 2 + SizeSmallSecondLine, _
- Yorigin + MarkerLabelPosition * EchelleVert + 5)
- '.Name = "Markline_" & MarkerNumber
- End With
- With ActiveSheet.Shapes.AddShape(msoShapeRectangle, _
- Xorigin + (MarkerChromosome - FirstChromosome) * ChrSpace + SizeSmallSecondLine, _
- Yorigin + MarkerLabelPosition * EchelleVert, _
- 120#, MyFontSize * 2)
- .TextFrame.Characters.Text = MarkerName & " (" & Format(MarkerPosition, "###0.0") & ")"
- .Fill.Visible = False
- .Line.Visible = False
- '.TextFrame.Characters.Font.Name = MyfontName
- '.TextFrame.Characters.Font.Size = MyfontSize
- .Name = "Mark_" & MarkerNumber
- End With
-Next Row
-
-Dim MyTime2: MyTime2 = Time: TempsEcoule = MyTime2 - MyTime
-ActiveWindow.Zoom = 100
-'Application.CommandBars("Map Zoom").Visible = True
-ThisWorkbook.Sheets("DrawSimulMap").Activate
-ResetFontIndicator
-ResetFontSize
-1000 Application.StatusBar = False
-
-End Sub
-
-
-Public Sub Read_Chr_Simulated()
-Application.ScreenUpdating = False
-ThisWorkbook.Sheets("SimulMap").Activate
-
-Range("B6", Range("B1048576").End(xlUp)).Select
-NbOfRows = Selection.Rows.Count
-
-Range("J27:N1000").ClearContents
-
-NumbOfMarkInChrTotal = 0
-TotalMapSize = 0
-NumberOfChr = 0
-For i = 6 To NbOfRows + 6
- If Cells(i + 1, 2) <> Cells(i, 2) Then 'new chr is detected
- NumberOfChr = NumberOfChr + 1
- Cells(26 + Cells(i, 2), 10) = Cells(i, 2) 'chr number
- ChrSize = Cells(i, 5)
- Cells(26 + Cells(i, 2), 11) = ChrSize 'chr size
- TotalMapSize = TotalMapSize + Cells(i, 5)
- NumbOfMarkInChr = i - 5 - NumbOfMarkInChrTotal
- Cells(26 + Cells(i, 2), 12) = NumbOfMarkInChr
- MarkerDensity = ChrSize / NumbOfMarkInChr
- Cells(26 + Cells(i, 2), 14) = MarkerDensity
- NumbOfMarkInChrTotal = NumbOfMarkInChrTotal + NumbOfMarkInChr
- End If
-Next
-[N22] = TotalMapSize
-[N23] = NumbOfMarkInChrTotal
-[N24] = TotalMapSize / NumbOfMarkInChrTotal
-[R22] = NumberOfChr
-
-[N22].Select
-Application.ScreenUpdating = True
-End Sub
-
-Public Sub Add_Simulated_To_Map_1()
-Application.ScreenUpdating = False
- Sheets("SimulMap").Activate
- Range("B6:F6").Select
- Range(Selection, Selection.End(xlDown)).Select
- Copy_Values_MD
- Range("B6").Select
- Sheets("CompMap").Activate
- Range("B6:f1048576").Select
- Selection.ClearContents
- Range("B6").Select
-' ActiveSheet.Paste
- Paste_Values_MD
- Range("B6").Select
-End Sub
-
-Public Sub Add_Simulated_To_Map_2()
-Application.ScreenUpdating = False
- Sheets("SimulMap").Activate
- Range("B6:F6").Select
- Range(Selection, Selection.End(xlDown)).Select
- Copy_Values_MD
- Range("B6").Select
- Sheets("CompMap").Activate
- Range("H6:L1048576").Select
- Selection.ClearContents
- Range("H6").Select
-' ActiveSheet.Paste
- Paste_Values_MD
- Range("H6").Select
-End Sub
-
-
-Public Sub BatchMap()
-'Reads a series of mapmaker/EXP compatible data files, computes the map and reports a summary
-'Assumes that the linkage group are already defined and ordered.
-'Needs to have the sequences pasted in My sequences
-'Max 254 genotypes
-
-'On Error GoTo 900
-Dim MyTime
-MyTime = Time
-BatchMode = 1
-AutoBatchMapOn = 0
-
-Application.ScreenUpdating = False
-
-msg = "Are you sure you want to continue? This will clear the previous batch results and the current sequences."
-Style = vbYesNo
-Title = "Confirmation"
-Ctxt = 1000
-response = MsgBox(msg, Style, Title)
-If response = vbNo Then GoTo 1100
-
-If ThisWorkbook.Sheets("SimulMap").[b6] = "" Then MsgBox ("Please simulate a map first"): GoTo 1100
-
-ThisWorkbook.Sheets("Menus").Range("N24:IV1023").ClearContents
-ThisWorkbook.Sheets("Menus").Range("J24:J1023").ClearContents
-
-CopySequencesFromSimulatedMap
-
-nbseq = ThisWorkbook.Sheets("Menus").Cells(23, 19)
-If nbseq = 0 Then
- MsgBox ("Please simulate a map first")
- ActiverSimulate
- GoTo 1100
-End If
-
-Application.StatusBar = "reading Menu"
-MenuMatrix = ThisWorkbook.Sheets("Menus").UsedRange.Value
-
-Read_Mapping_Options
-
-If ThisWorkbook.Sheets("Data").[D4] <> "" And ThisWorkbook.Sheets("Data").[c16] <> "" Then
- msg = "Do you want to store the data that are in the 'Data' window before importation?"
- Style = vbYesNo + vbCritical + vbDefaultButton1
- Title = "Import Mapmaker data"
- Ctxt = 1000
- response = MsgBox(msg, Style, Title)
- If response = vbYes Then Store_Data
-End If
-
-Application.StatusBar = "Erasing current data"
-ThisWorkbook.Sheets("Data").Range("B15:IV60000").ClearContents
-'ThisWorkbook.Sheets("Data+").Range("B15:IV60000").ClearContents
-
-NumberOfFilesToProcess = ThisWorkbook.Sheets("SimulMap").[n3]
-If NumberOfFilesToProcess > MaxNumberOfColumns - 7 Then BigBatchMode = 1 Else BigBatchMode = 0
-
-NbLocus = ThisWorkbook.Sheets("SimulMap").[N23]
-Indiv = ThisWorkbook.Sheets("SimulMap").[N17]
-
-myfilename = Application.GetOpenFilename(Title:="Locate the SimulPop_1.txt file")
-If myfilename = False Then GoTo 1100
-Workbooks.OpenText Filename:=myfilename, DataType:=xlDelimited, Tab:=True, Space:=True, ConsecutiveDelimiter:=True
-
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
- ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
- ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
- ThisWorkbook.Sheets("BatchMap").Range("C8:G60000").Interior.ColorIndex = xlNone
- ThisWorkbook.Sheets("BatchMap").Range("H5:IV6").Interior.ColorIndex = xlNone
- ReDim BatchResults(NbLocus + 1, NumberOfFilesToProcess) As Variant
-Else
- ThisWorkbook.Sheets("BigBatch").Range("C6:D60000").ClearContents
- ReDim BigBatchResults(NumberOfFilesToProcess, 2) As Variant
-End If
-
-LengthOfPath = Len(myfilename)
-OutputPath = Left(myfilename, LengthOfPath - 5)
-myfilename = ActiveWorkbook.Name
-Workbooks(myfilename).Close savechanges:=False
-
-For CurrentPopulation = 1 To NumberOfFilesToProcess
- 'Application.StatusBar = "Population " & CurrentPopulation & ":" ' Importing data file
- Import_Mapmaker_data_For_Batch
- Application.StatusBar = "Population " & CurrentPopulation & ": Computing map"
- ComputeMapForAutoBatch
- 'If BigBatchMode = 0 Then ThisWorkbook.Sheets("BatchMap").Cells(7, CurrentPopulation + 7) = "Pop" & CurrentPopulation
- If BigBatchMode = 0 Then BatchResults(0, CurrentPopulation - 1) = "Pop" & CurrentPopulation
-Next
-
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Activate
- ThisWorkbook.Sheets("BatchMap").[D4] = NumberOfFilesToProcess
- NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
- ThisWorkbook.Sheets("BatchMap").[f4] = NumberOfMarkers
- [h7].Resize(NbLocus + 3, NumberOfFilesToProcess) = BatchResults
- ThisWorkbook.Sheets("SimulMap").Activate
- Range("D6").Select
- Range(Selection, Selection.End(xlDown)).Select
- Selection.Copy
- [N22].Select
- ThisWorkbook.Sheets("BatchMap").Activate
- Range("B8").Select
- Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
- :=False, Transpose:=False
-
- Compute_Stats_Batch
-Else
- ThisWorkbook.Sheets("BigBatch").Activate
- [c6].Resize(NumberOfFilesToProcess, 2) = BigBatchResults
-End If
-
-Dim MyTime2
-MyTime2 = Time
-TempsEcoule = MyTime2 - MyTime
-Application.StatusBar = "Batchmap total time was " & Format(TempsEcoule, "h:mm:ss")
-
-GoTo 1000
-900 MsgBox "An error occurred during the BatchMap procedure."
-GoTo 1100
-1000
-BatchMode = 0
-'Application.StatusBar = False
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Activate
-Else
- ThisWorkbook.Sheets("BigBatch").Activate
-End If
-
-Beep
-[h8].Select
-1100
-End Sub
-
-
-Public Sub Auto_Batch_Map()
-'Same than BatchMap but simulates populations at the same time so saves CPU time
-'Simulates a series of populations, computes the map and reports a summary
-'Assumes that the linkage groups are already defined and ordered.
-'Needs to have the sequences pasted in My sequences
-
-'On Error GoTo 900
-Dim MyTime
-MyTime = Time
-BatchMode = 1
-AutoBatchMapOn = 1
-
-Application.ScreenUpdating = False
-
-msg = "Are you sure you want to continue? This will clear the previous batch results and the current sequences."
-Style = vbYesNo
-Title = "Confirmation"
-Ctxt = 1000
-response = MsgBox(msg, Style, Title)
-If response = vbNo Then GoTo 1100
-
-If ThisWorkbook.Sheets("SimulMap").[b6] = "" Then MsgBox ("Please simulate a map first"): GoTo 1100
-
-ThisWorkbook.Sheets("Menus").Range("N24:IV1023").ClearContents
-ThisWorkbook.Sheets("Menus").Range("J24:J1023").ClearContents
-
-CopySequencesFromSimulatedMap
-
-nbseq = ThisWorkbook.Sheets("Menus").Cells(23, 19)
-If nbseq = 0 Then
- MsgBox ("Please simulate a map first")
- ActiverSimulate
- GoTo 1100
-End If
-
-Application.StatusBar = "reading Menu "
- MenuMatrix = ThisWorkbook.Sheets("Menus").UsedRange.Value
-Application.StatusBar = "reading simulation parameters"
- VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
- Read_Simulation_Parameters
-
-If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" And SimulatedPopulationType <> "BC2F1" And SimulatedPopulationType <> "SSD" Then MsgBox "BC1 or F2 populations only, sorry.": GoTo 1000
-
-Application.StatusBar = "reading mapping options"
- Read_Mapping_Options
-
-NumberOfFilesToProcess = ThisWorkbook.Sheets("SimulMap").[n3]
-
-BigBatchMode = 0
-If MaxNumberOfColumns = 256 Then
- If NumberOfFilesToProcess > 249 Then BigBatchMode = 1 Else BigBatchMode = 0
-End If
-
-NbLocus = ThisWorkbook.Sheets("SimulMap").[N23]
-Indiv = ThisWorkbook.Sheets("SimulMap").[N17]
-
-ReDim Data(Indiv, NbLocus) As Variant
-Application.StatusBar = "Clearing"
-
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
- ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
- ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
- ThisWorkbook.Sheets("BatchMap").Range("C8:G60000").Interior.ColorIndex = xlNone
- ThisWorkbook.Sheets("BatchMap").Range("H5:XFD60000").Interior.ColorIndex = xlNone
- ReDim BatchResults(NbLocus + 1, NumberOfFilesToProcess) As Variant
-Else
- ThisWorkbook.Sheets("BigBatch").Range("C6:D60000").ClearContents
- ReDim BigBatchResults(NumberOfFilesToProcess, 2) As Variant
-End If
-
-For CurrentPopulation = 1 To NumberOfFilesToProcess
- Application.StatusBar = "Processing population " & CurrentPopulation
- Simulate_Population_From_Map
- ComputeMapForAutoBatch
- 'If BigBatchMode = 0 Then ThisWorkbook.Sheets("BatchMap").Cells(7, CurrentPopulation + 7) = "Pop" & CurrentPopulation
- If BigBatchMode = 0 Then BatchResults(0, CurrentPopulation - 1) = "Pop" & CurrentPopulation
-Next
-
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Activate
- [D4] = NumberOfFilesToProcess
- NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
- [f4] = NumberOfMarkers
- [h7].Resize(NbLocus + 3, NumberOfFilesToProcess) = BatchResults
- ThisWorkbook.Sheets("SimulMap").Activate
- Range("D6").Select
- Range(Selection, Selection.End(xlDown)).Select
- Selection.Copy
- [N22].Select
- ThisWorkbook.Sheets("BatchMap").Activate
- Range("B8").Select
- Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
- :=False, Transpose:=False
-
- Compute_Stats_Batch
-Else
- ThisWorkbook.Sheets("BigBatch").Activate
- [c6].Resize(NumberOfFilesToProcess, 2) = BigBatchResults
-End If
-
-Dim MyTime2
-MyTime2 = Time
-TempsEcoule = MyTime2 - MyTime
-Application.StatusBar = "Autobatchmap total time was " & Format(TempsEcoule, "h:mm:ss")
-GoTo 1000
-900 MsgBox "An error occurred during the AutoBatchMap procedure."
-GoTo 1100
-1000
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Activate
-Else
- ThisWorkbook.Sheets("BigBatch").Activate
-End If
-AutoBatchMapOn = 0
-BigBatchMode = 1
-'Application.StatusBar = False
-Beep
-[h8].Select
-1100
-End Sub
-
-
-Public Sub Auto_Batch_Map_Chi2()
-'Same than BatchMap but simulates populations at the same time so saves CPU time
-'Simulates a series of populations, computes the map and reports a summary
-'Assumes that the linkage groups are already defined and ordered.
-'Needs to have the sequences pasted in My sequences
-
-'On Error GoTo 900
-Dim MyTime
-MyTime = Time
-BatchMode = 1
-AutoBatchMapOn = 1
-
-Application.ScreenUpdating = False
-
-msg = "Are you sure you want to continue? This will clear the previous batch results and the current sequences."
-Style = vbYesNo
-Title = "Confirmation"
-Ctxt = 1000
-response = MsgBox(msg, Style, Title)
-If response = vbNo Then GoTo 1100
-
-If ThisWorkbook.Sheets("SimulMap").[b6] = "" Then MsgBox ("Please simulate a map first"): GoTo 1100
-
-ThisWorkbook.Sheets("Menus").Range("N24:IV1023").ClearContents
-ThisWorkbook.Sheets("Menus").Range("J24:J1023").ClearContents
-
-CopySequencesFromSimulatedMap
-
-nbseq = ThisWorkbook.Sheets("Menus").Cells(23, 19)
-If nbseq = 0 Then
- MsgBox ("Please simulate a map first")
- ActiverSimulate
- GoTo 1100
-End If
-
-Application.StatusBar = "reading Menu "
- MenuMatrix = ThisWorkbook.Sheets("Menus").UsedRange.Value
-Application.StatusBar = "reading simulation parameters"
- VirtualMap = ThisWorkbook.Sheets("SimulMap").UsedRange.Value
- Read_Simulation_Parameters
-
-If SimulatedPopulationType <> "BC1" And SimulatedPopulationType <> "F2" And SimulatedPopulationType <> "BC2F1" And SimulatedPopulationType <> "SSD" Then MsgBox "BC1 or F2 populations only, sorry.": GoTo 1000
-
-Application.StatusBar = "reading mapping options"
- Read_Mapping_Options
-
-NumberOfFilesToProcess = ThisWorkbook.Sheets("SimulMap").[n3]
-
-BigBatchMode = 0
-If MaxNumberOfColumns = 256 Then
- If NumberOfFilesToProcess > 249 Then BigBatchMode = 1 Else BigBatchMode = 0
-End If
-
-NbLocus = ThisWorkbook.Sheets("SimulMap").[N23]
-Indiv = ThisWorkbook.Sheets("SimulMap").[N17]
-
-ReDim Data(Indiv, NbLocus) As Variant
-
-Application.StatusBar = "Clearing"
-
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Range("A5:IV60000").ClearContents
- ThisWorkbook.Sheets("BatchMap").[D4].ClearContents
- ThisWorkbook.Sheets("BatchMap").[f4].ClearContents
- ThisWorkbook.Sheets("BatchMap").Range("C5:XFD60000").Interior.ColorIndex = xlNone
- 'ThisWorkbook.Sheets("BatchMap").Range("H5:XFD7").Interior.ColorIndex = xlNone
- ReDim BatchResults(NbLocus + 1, NumberOfFilesToProcess) As Variant
-Else
- ThisWorkbook.Sheets("BigBatch").Range("C6:D60000").ClearContents
- ReDim BigBatchResults(NumberOfFilesToProcess, 2) As Variant
-End If
-
-For CurrentPopulation = 1 To NumberOfFilesToProcess
- Application.StatusBar = "Processing population " & CurrentPopulation
- Simulate_Population_From_Map
- 'ComputeMapForAutoBatch
-
- ComputeChiSquareForAutoBatch
-
- 'If BigBatchMode = 0 Then ThisWorkbook.Sheets("BatchMap").Cells(7, CurrentPopulation + 7) = "Pop" & CurrentPopulation
- If BigBatchMode = 0 Then BatchResults(0, CurrentPopulation - 1) = "Pop" & CurrentPopulation
-Next
-
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Activate
- [D4] = NumberOfFilesToProcess
- NumberOfMarkers = ThisWorkbook.Sheets("SimulMap").[N23]
- [f4] = NumberOfMarkers
-
- [h7].Resize(NbLocus + 3, NumberOfFilesToProcess) = BatchResults
-
- ThisWorkbook.Sheets("SimulMap").Activate
- Range("D6").Select
- Range(Selection, Selection.End(xlDown)).Select
- Selection.Copy
- [N22].Select
- ThisWorkbook.Sheets("BatchMap").Activate
- Range("B8").Select
- Selection.PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, SkipBlanks _
- :=False, Transpose:=False
-
- Compute_Stats_Batch_Chi2
-Else
- ThisWorkbook.Sheets("BigBatch").Activate
- [c6].Resize(NumberOfFilesToProcess, 2) = BigBatchResults
-End If
-
-Dim MyTime2
-MyTime2 = Time
-TempsEcoule = MyTime2 - MyTime
-Application.StatusBar = "Autobatchmap total time was " & Format(TempsEcoule, "h:mm:ss")
-GoTo 1000
-900 MsgBox "An error occurred during the AutoBatchMap procedure."
-GoTo 1100
-1000
-If BigBatchMode = 0 Then
- ThisWorkbook.Sheets("BatchMap").Activate
-Else
- ThisWorkbook.Sheets("BigBatch").Activate
-End If
-AutoBatchMapOn = 0
-BigBatchMode = 1
-'Application.StatusBar = False
-Beep
-[h8].Select
-1100
-End Sub
-
--
GitLab