beadarrayMSV-package	beadarrayMSV-package
AlleleSetIllumina-class	AlleleSetIllumina-class
assignParalogues	assignParalogues
assignToAlleleSet	createAlleleSet
beadarrayMSV	beadarrayMSV-package
BeadSetIllumina-class	BeadSetIllumina-class
BSRed.193	BSRed.193
callGenotypes	callGenotypes
callGenotypes.interactive	callGenotypes
callGenotypes.verboseTest	callGenotypes
cart2pol	cart2pol
countFailedSNP	countFailedSNP
createAlleleSet	createAlleleSet
createAlleleSetFromFiles	createAlleleSet
createMultiSetFromFiles	createAlleleSet
findClusters	findClusters
findPolyploidClusters	findPolyploidClusters
findSeTheta	findSeTheta
generatePolyCenters	generatePolyCenters
getCenters	getCenters
getNoiseDistributions	getNoiseDistributions
getNormInd	getNormInd
getSingleCalls	getSingleCalls
getSpecificCenters	getCenters
initialize,AlleleSetIllumina-method	AlleleSetIllumina-class
initialize,BeadSetIllumina-method	BeadSetIllumina-class
locateParalogues	locateParalogues
makeDiploidCalls	makeDiploidCalls
makeFilenames	makeFilenames
manualCall	manualCall
modifyExistingFilenames	makeFilenames
normalizeIllumina	shearRawSignal
normalizeShearedChannels	normalizeShearedChannels
plotCountsChrom	locateParalogues
plotEstimatedNoise	getNoiseDistributions
plotGenotypes	plotGenotypes
plotPreprocessing	preprocessBeadSet
preprocessBeadSet	preprocessBeadSet
readBeadSummaryOutput	readBeadSummaryOutput
resolveInheritanceSNP	resolveInheritanceSNP
scatterArrays	scatterArrays
setGenoOptions	callGenotypes
setMergeOptions	assignParalogues
setNormOptions	preprocessBeadSet
shearRawSignal	shearRawSignal
testHardyWeinberg	testHardyWeinberg
transformChannels	transformChannels
transformSEs	transformChannels
translateTheta	translateTheta
translateThetaCombined	translateTheta
translateThetaFromFiles	translateTheta
unmixParalogues	unmixParalogues
validateCallsPedigree	validateCallsPedigree
validateSingleCall	validateCallsPedigree
writeAlleleSet	writeAlleleSet
