validateCallsPedigree: Pedigree validation of genotypes

In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

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 callGenotypes), or alternatively a column “Manual.Calls.R” (see callGenotypes.interactive). It must also contain a phenoData column “PedigreeID”. This 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
marker	Data frame with at least the columns “Call” and “PedigreeID” for a single marker. The first corresponds to the "AlleleSetIllumina" assayData entry “call”, the latter is described above.
classification	Character string with genotype call category for the marker (see generatePolyCenters)

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.

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

Author(s)

Lars Gidskehaug

See Also

callGenotypes, plotGenotypes

Examples

## Not run: 
#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)

## End(Not run)

beadarrayMSV documentation built on May 1, 2019, 6:33 p.m.