getSingleCalls: Identify MSV-5 paralogs with equal genotypes

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

View source: R/beadarrayMSV.R

Description

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

Usage

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Arguments

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

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.

Value

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

Author(s)

Lars Gidskehaug

See Also

unmixParalogues, assignParalogues, AlleleSetIllumina, callGenotypes

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 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)

beadarrayMSV documentation built on May 29, 2017, 9:07 a.m.