"BeadSetIllumina " and
"AlleleSetIllumina ", are defined for holding and
working with genetic data.Illumina BeadArray summary-data are loaded using the function
readBeadSummaryOutput, and pre-processed using
preprocessBeadSet.
Automatic clustering and genotype calling is performed using
callGenotypes, and validated using
validateCallsPedigree and plotGenotypes.
Manual clustering with callGenotypes.interactive, which
benefits from the interactive graphics package assignToAlleleSet.
Reading and writing data from and to files with the functions
createAlleleSetFromFiles and
writeAlleleSet.
For splitting MSV-5 markers into individual paralogs and assigning them to
chromosomes, use assignParalogues.