Based on parental and offspring SNP marker genotypes, the paternal and maternal alleles in offspring are deduced
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
assignParalogues). For its
BSSnp should therefore contain chromosome
positions and genetic distances in
A list with elements
Matrix of calls representing maternal inherited alleles
Matrix of calls representing paternal inherited alleles
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
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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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