beadarrayMSV (version 1.0.3)

validateCallsPedigree: Pedigree validation of genotypes

Description

Checks that genotypes follow basic rules of inheritance

Usage

validateCallsPedigree(BSRed)
validateSingleCall(marker, classification)

Arguments

BSRed

"AlleleSetIllumina" object containing an assayData entry call as well as a featureData column Classification (see

marker

Data frame with at least the columns Call and PedigreeID for a single marker. The first corresponds to the "AlleleSetIllumina" assayData entry call<

classification

Character string with genotype call category for the marker (see generatePolyCenters)

Value

• Output from validateCallsPedigree is an "AlleleSetIllumina" object with an added assayData entry ped.check. This logical matrix is FALSE for all offspring violating the pedigree information, an all parents are NA Output from validateSingleCall is a numeric vector with {0, 1, 2} denoting no error, offspring error, and parent error, respectively

Details

validateCallsPedigree is usually faster and easier to use compared to validateSingleCall. The latter is more often called by other functions, however it has a slightly more detailed outut.

See Also

callGenotypes, plotGenotypes

Examples

#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, pedigree validation and plotting
BSRed <- callGenotypes(BSRed)
BSRed <- validateCallsPedigree(BSRed)
plotGenotypes(BSRed,1:25)