Track parental alleles in offspring

Description

Based on parental and offspring SNP marker genotypes, the paternal and maternal alleles in offspring are deduced

Usage

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Arguments

BSSnp

"AlleleSetIllumina" (or "MultiSet") object containing only SNP markers, with an assayData entry “call” (see callGenotypes) and a phenoData column “PedigreeID”. The latter contains strings <p><mmm><fff><oo>, where “p”, “mmm”, “fff”, and “oo” are unique identifiers for population, mother, father, and individual within full-sib group, respectively. “000” means founding parent, whereas “999” means unknown parent

Details

Although a linkage map is not needed for this function, it was written for the purpose of mapping MSV-5 paralogs to a map represented by the markers in BSSnp (see assignParalogues). For its intended use, BSSnp should therefore contain chromosome positions and genetic distances in featureData

Value

A list with elements

mother

Matrix of calls representing maternal inherited alleles

father

Matrix of calls representing paternal inherited alleles

Note

Offspring alleles from monomorpic parents are sometimes missing even though the inherited alleles can be directly deduced from the parental genotype. This is for efficiency of the algorithm, as monomorphic parents carry no linkage information

Author(s)

Lars Gidskehaug

See Also

AlleleSetIllumina, callGenotypes, assignParalogues, unmixParalogues

Examples

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## Not run: 
#Read markers into an AlleleSetIllumina object
rPath <- system.file("extdata", package="beadarrayMSV")
normOpts <- setNormOptions()
dataFiles <- makeFilenames('testdata',normOpts,rPath)
beadFile <- paste(rPath,'beadData_testdata.txt',sep='/')
beadInfo <- read.table(beadFile,sep='\t',header=TRUE,as.is=TRUE)
BSRed <- createAlleleSetFromFiles(dataFiles[1:4],beadInfo=beadInfo)

#Genotype calling and selection of SNPs for linkage map
BSRed <- callGenotypes(BSRed)
BSRed <- validateCallsPedigree(BSRed)
iSNP <- fData(BSRed)$Classification %in% 'SNP' &! is.na(fData(BSRed)$Chromosome)

#Find informative alleles inherited from each parent
inheritP <- resolveInheritanceSNP(BSRed[iSNP,])

#Compare a few markers for an arbitrary, single triplet
iOffspring <- 1
iFather <- which(pData(BSRed)$PedigreeID %in% pData(BSRed)$Parent2[iOffspring])
iMother <- which(pData(BSRed)$PedigreeID %in% pData(BSRed)$Parent1[iOffspring])
print(assayData(BSRed)$call[iSNP,c(iMother,iFather,iOffspring)][6:10,])
print(inheritP$mother[6:10,c(iMother,iFather,iOffspring)])
print(inheritP$father[6:10,c(iMother,iFather,iOffspring)])

## End(Not run)

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