Description Usage Arguments Details Value Note Author(s) See Also Examples
Based on parental and offspring SNP marker genotypes, the paternal and maternal alleles in offspring are deduced
1 | resolveInheritanceSNP(BSSnp)
|
BSSnp |
|
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
A list with elements
mother |
Matrix of calls representing maternal inherited alleles |
father |
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
Lars Gidskehaug
AlleleSetIllumina
, callGenotypes
,
assignParalogues
, unmixParalogues
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ## 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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