getSingleCalls: Identify MSV-5 paralogs with equal genotypes
In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Description Usage Arguments Details Value Author(s) See Also Examples

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

1	getSingleCalls(BSRed)

BSRed

"AlleleSetIllumina" (or "MultiSet") object containing only MSV-5 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

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.

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

Lars Gidskehaug

unmixParalogues, assignParalogues, AlleleSetIllumina, callGenotypes

## 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 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])

## End(Not run)