beadarrayMSV (version 1.0.3)

getSingleCalls: Identify MSV-5 paralogs with equal genotypes

Description

Identifies MSV-5 markers for which both paralogs are either AA, BB, or AB

Usage

getSingleCalls(BSRed)

Arguments

BSRed

"AlleleSetIllumina" (or "MultiSet") object containing only MSV-5 markers, with an assayData entry call (see

Value

• Matrix of size dim(BSRed) containing calls in {0, 1/2, 1} for the markers in question, NA otherwise

Details

For use in other functions, such as unmixParalogues and assignParalogues. May be called initially by user in order to save time in the subsequent calculations. All monomorphic markers [AA,AA] and [BB,BB], as well as parental markers with genotype [AB,AB] are identified.

See Also

unmixParalogues, assignParalogues, AlleleSetIllumina, callGenotypes

Examples

#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 some MSV-5s
BSRed <- callGenotypes(BSRed)
BSRed <- validateCallsPedigree(BSRed)
iMSV5 <- fData(BSRed)$Classification %in% 'MSV-5' &
    fData(BSRed)$Ped.Errors %in% 0
plotGenotypes(BSRed,markers=which(iMSV5))

#Find markers in question and compare
singleCalls <- getSingleCalls(BSRed[iMSV5,])
print(assayData(BSRed)$call[iMSV5,1:4])
print(singleCalls[,1:4])