Nothing
# Wrapper functions that run multiple steps in a pipeline for polyRAD
IterateHWE <- function(object, selfing.rate = 0, tol = 1e-5,
excludeTaxa = GetBlankTaxa(object),
overdispersion = 9){
if(!"RADdata" %in% class(object)){
stop("RADdata object needed.")
}
if(tol > 1e-2){
warning("tol unexpectedly high.")
}
if(tol < 0){
stop("tol must be above zero")
}
nIter <- 1 # which round of iteration are we on
meanDiff <- 1 # mean difference between allele frequencies from round to round
# (1 is a dummy value for while loop)
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
while(meanDiff > tol){
message(paste("Starting iteration", nIter))
oldAlFreq <- object$alleleFreq
object <- AddGenotypePriorProb_HWE(object, selfing.rate)
object <- AddGenotypeLikelihood(object, overdispersion = overdispersion)
object <- AddPloidyChiSq(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePosteriorProb(object)
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
nIter <- nIter + 1
meanDiff <- mean(abs(oldAlFreq - object$alleleFreq), na.rm = TRUE)
message(paste("Mean difference in allele frequencies of", meanDiff))
}
return(object)
}
IterateHWE_LD <- function(object, selfing.rate = 0, tol = 1e-5,
excludeTaxa = GetBlankTaxa(object),
LDdist = 1e4, minLDcorr = 0.2,
overdispersion = 9){
if(!"RADdata" %in% class(object)){
stop("RADdata object needed.")
}
if(tol > 1e-2){
warning("tol unexpectedly high.")
}
if(tol < 0){
stop("tol must be above zero")
}
nIter <- 1 # which round of iteration are we on
meanDiff <- 1 # mean difference between allele frequencies from round to round
# (1 is a dummy value for while loop)
message("Performing preliminary genotype estimation.")
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePriorProb_HWE(object, selfing.rate)
object <- AddGenotypeLikelihood(object, overdispersion = overdispersion)
object <- AddPloidyChiSq(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePosteriorProb(object)
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
message("Finding alleles in LD.")
object <- AddAlleleLinkages(object, type = "hwe",
linkageDist = LDdist, minCorr = minLDcorr,
excludeTaxa = GetBlankTaxa(object))
while(meanDiff > tol){
message(paste("Starting iteration", nIter))
oldAlFreq <- object$alleleFreq
object <- AddGenotypePriorProb_HWE(object, selfing.rate)
object <- AddGenotypePriorProb_LD(object, type = "hwe")
object <- AddGenotypeLikelihood(object, overdispersion = overdispersion)
object <- AddPloidyChiSq(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePosteriorProb(object)
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
nIter <- nIter + 1
meanDiff <- mean(abs(oldAlFreq - object$alleleFreq), na.rm = TRUE)
message(paste("Mean difference in allele frequencies of", meanDiff))
}
return(object)
}
IteratePopStruct <- function(object, selfing.rate = 0, tol = 1e-3,
excludeTaxa = GetBlankTaxa(object),
nPcsInit = 10, minfreq = 0.0001,
overdispersion = 9, maxR2changeratio = 0.05){
if(!"RADdata" %in% class(object)){
stop("RADdata object needed.")
}
if(tol > 1e-2){
warning("tol unexpectedly high.")
}
if(tol < 0){
stop("tol must be above zero")
}
nIter <- 1 # which round of iteration are we on
meanDiff <- 1 # mean difference between allele frequencies from round to round
# (1 is a dummy value for while loop)
message("Performing initial PCA and allele frequency estimation.")
object <- AddPCA(object, nPcsInit = nPcsInit, maxR2changeratio = maxR2changeratio)
object <- AddAlleleFreqByTaxa(object)
while(meanDiff > tol){
message(paste("Starting iteration", nIter))
message(paste("PCs used:", dim(object$PCA)[2]))
oldAlFreq <- object$alleleFreqByTaxa
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePriorProb_ByTaxa(object, selfing.rate)
object <- AddGenotypeLikelihood(object, overdispersion = overdispersion)
object <- AddPloidyChiSq(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePosteriorProb(object)
object <- AddPCA(object, nPcsInit = dim(object$PCA)[2] + 1,
minPcsOut = dim(object$PCA)[2],
maxR2changeratio = maxR2changeratio)
# -> reasoning for PC number constraints:
# tend to get more accuracy with more PCs,
# number of PCs going up and down prevents convergence of algorithm
object <- AddAlleleFreqByTaxa(object, minfreq = minfreq)
nIter <- nIter + 1
meanDiff <- mean(abs(oldAlFreq - object$alleleFreqByTaxa), na.rm = TRUE)
message(paste("Mean difference in allele frequencies of", meanDiff))
}
return(object)
}
# Function to run genotype estimation using both population structure and
# linkage disequilibrium.
# LDdist is the distance in nucleotides within which to search for alleles in LD.
# minLDcorr is the minimum correlation coefficient between the residuals of
# allelic values after regression on PCA axes, with the values of a nearby
# allele, for that allele to be used in genotype prediction.
IteratePopStructLD <- function(object, selfing.rate = 0, tol = 1e-3,
excludeTaxa = GetBlankTaxa(object),
nPcsInit = 10, minfreq = 0.0001,
LDdist = 1e4, minLDcorr = 0.2,
overdispersion = 9, maxR2changeratio = 0.05){
if(!"RADdata" %in% class(object)){
stop("RADdata object needed.")
}
if(tol > 1e-2){
warning("tol unexpectedly high.")
}
if(tol < 0){
stop("tol must be above zero")
}
nIter <- 1 # which round of iteration are we on
meanDiff <- 1 # mean difference between allele frequencies from round to round
# (1 is a dummy value for while loop)
# Initialization before testing for LD
message("Performing initial PCA and allele frequency estimation.")
object <- AddPCA(object, nPcsInit = nPcsInit, maxR2changeratio = maxR2changeratio)
object <- AddAlleleFreqByTaxa(object)
message("Performing preliminary genotype estimation.")
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePriorProb_ByTaxa(object, selfing.rate)
object <- AddGenotypeLikelihood(object, overdispersion = overdispersion)
object <- AddPloidyChiSq(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePosteriorProb(object)
object <- AddPCA(object, nPcsInit = dim(object$PCA)[2] + 1,
minPcsOut = dim(object$PCA)[2],
maxR2changeratio = maxR2changeratio)
object <- AddAlleleFreqByTaxa(object, minfreq = minfreq)
# Test for LD
message("Finding alleles in LD.")
object <- AddAlleleLinkages(object, type = "popstruct",
linkageDist = LDdist, minCorr = minLDcorr,
excludeTaxa = GetBlankTaxa(object))
# Iteratively estimate genotypes
while(meanDiff > tol){
message(paste("Starting iteration", nIter))
message(paste("PCs used:", dim(object$PCA)[2]))
oldAlFreq <- object$alleleFreqByTaxa
object <- AddAlleleFreqHWE(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePriorProb_ByTaxa(object, selfing.rate)
object <- AddGenotypePriorProb_LD(object, type = "popstruct")
object <- AddGenotypeLikelihood(object, overdispersion = overdispersion)
object <- AddPloidyChiSq(object, excludeTaxa = excludeTaxa)
object <- AddGenotypePosteriorProb(object)
object <- AddPCA(object, nPcsInit = dim(object$PCA)[2] + 1,
minPcsOut = dim(object$PCA)[2],
maxR2changeratio = maxR2changeratio)
# -> reasoning for PC number constraints:
# tend to get more accuracy with more PCs,
# number of PCs going up and down prevents convergence of algorithm
object <- AddAlleleFreqByTaxa(object, minfreq = minfreq)
nIter <- nIter + 1
meanDiff <- mean(abs(oldAlFreq - object$alleleFreqByTaxa), na.rm = TRUE)
message(paste("Mean difference in allele frequencies of", meanDiff))
}
return(object)
}
PipelineMapping2Parents <- function(object,
n.gen.backcrossing = 0,
n.gen.intermating = 0,
n.gen.selfing = 0,
minLikelihoodRatio = 10,
freqAllowedDeviation = 0.05,
freqExcludeTaxa = c(GetDonorParent(object),
GetRecurrentParent(object),
GetBlankTaxa(object)),
useLinkage = TRUE, linkageDist = 1e7,
minLinkageCorr = 0.5,
overdispersion = 9){
if(useLinkage && (is.null(object$locTable$Chr) ||
is.null(object$locTable$Pos))){
stop("Set useLinkage = FALSE if alignment data unavailable.")
}
donorParent <- GetDonorParent(object)
recurrentParent <- GetRecurrentParent(object)
pld.don <- GetTaxaPloidy(object)[donorParent]
pld.rec <- GetTaxaPloidy(object)[recurrentParent]
# estimate possible allele frequencies
message("Making initial parameter estimates...")
pld.max <- max(sapply(object$possiblePloidies, sum))
allelesin <- (pld.don + pld.rec) * pld.max / 2
possfreq <- seq(0, 1, length.out = (n.gen.backcrossing + 1) * allelesin + 1)
object <- AddAlleleFreqMapping(object, expectedFreqs = possfreq,
allowedDeviation = freqAllowedDeviation,
excludeTaxa = freqExcludeTaxa)
# calculations for rest of pipeline
object <- AddGenotypeLikelihood(object, overdispersion = overdispersion)
object <- AddGenotypePriorProb_Mapping2Parents(object, donorParent = donorParent,
recurrentParent = recurrentParent,
n.gen.backcrossing = n.gen.backcrossing,
n.gen.intermating = n.gen.intermating,
n.gen.selfing = n.gen.selfing,
minLikelihoodRatio = minLikelihoodRatio)
object <- AddPloidyChiSq(object, excludeTaxa = freqExcludeTaxa)
object <- AddGenotypePosteriorProb(object)
# add in linkage data if available
if(useLinkage){
message("Updating priors using linkage...")
# find linkages
object <- AddAlleleLinkages(object, type = "mapping",
linkageDist = linkageDist,
minCorr = minLinkageCorr,
excludeTaxa = freqExcludeTaxa)
# update genotype probabilities
object <- AddGenotypePriorProb_LD(object, type = "mapping")
object <- AddGenotypePosteriorProb(object)
} # end IF statement for using linked alleles
message("Done.")
return(object)
} # end PipelineMapping2Parents
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