makeDiploidCalls: Constrain calls to diploid representation
In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

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

Input calls for any diploid or tetraploid genome marker are restricted to diploid representation. This implies that non-segregating paralogs are ignored or set to missing, and non-resolvable paralogs are set to missing

1	makeDiploidCalls(calls, fData)

`calls`	Numerical matrix with dimensions (markers x samples). The allele ratios are from the set {0, 1/4, 1/2, 3/4, 1}
`fData`	`featureData` data-table such as from an `"AlleleSetIllumina"` object, with rows corresponding to rows in `calls` and containing the column “Classification” (see `callGenotypes`). A column “Manual.Calls.R” will be used if present (see `callGenotypes.interactive`)

Usually called by the function translateTheta

A numerical matrix with the same dimensions as calls, however with values restricted to {0, 1/2, 1}

Lars Gidskehaug

translateTheta, AlleleSetIllumina

#Construct tiny example data
calls <- c(0,.5,1,0,.25,.5,.5,.75,1,.5,.5,.5,0,.25,.75)
categories <- c('SNP','MSV-a','MSV-b','PSV','MSV-5')
calls <- matrix(calls,nrow=5,byrow=TRUE,
    dimnames=list(categories,paste('S',1:3,sep='')))
fData <- data.frame(Classification=categories,row.names=categories)
print(calls)

#Make diploid
diploidCalls <- makeDiploidCalls(calls, fData)
print(diploidCalls)