countFailedSNP: Calculate ratio of called markers for each array

Description

Not counting markers classified as FAIL or MONO-filt, calculate the ratio of markers that are called for each array

Usage

countFailedSNP(BSRed, inclPedErrors = TRUE)

Arguments

BSRed

"AlleleSetIllumina" object containing an assayData entry call (see callGenotypes)

inclPedErrors

If TRUE, calls violating pedigree count as missing

Value

An "AlleleSetIllumina" object with an added phenoData column passRatio. This is a numeric vector holding the ratio of non-missing calls for each array

Details

In order to include pedigree errors, BSRed must have an assayData entry ped.check (see validateCallsPedigree)

Examples

Run this code

#Read pre-processed data directly into 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
BSRed <- callGenotypes(BSRed)
BSRed <- validateCallsPedigree(BSRed)
BSRed <- countFailedSNP(BSRed,inclPedErrors=TRUE)
print(range(pData(BSRed)$passRatio))

#Plot highlighting markers to be discarded
#NB! Such a high passRatio is not recommended
indGoodArrays <- pData(BSRed)$passRatio > 0.6
plotGenotypes(BSRed,indHighlight=which(!indGoodArrays))