AlleleSetIllumina-class
                        Class to Contain Objects Describing
                        High-Throughput Illumina BeadArrays
BSRed.193               Atlantic salmon genotype data with mainly MSV-5
                        markers
BeadSetIllumina-class   Class to Contain Objects Describing
                        High-Throughput Illumina BeadArrays
assignParalogues        Assign MSV-5 paralogs to chromosomes
beadarrayMSV-package    beadarrayMSV: Package for analysis of
                        high-throughput Illumina BeadArrays
callGenotypes           Clustering and calling of genotypes
cart2pol                Transformation from Cartesian to polar
                        coordinates
countFailedSNP          Calculate ratio of called markers for each
                        array
createAlleleSet         Create AlleleSetIllumina or MultiSet objects
findClusters            Suggest clusters based on histograms
findPolyploidClusters   K-means clustering
findSeTheta             Scale pooled standard errors after polar
                        transformation
generatePolyCenters     Generate list of possible genotype categories
getCenters              Estimate starting points for clustering
getNoiseDistributions   Estimate median and robust spread of background
                        noise
getNormInd              Retrieve sub-bead pool indexes
getSingleCalls          Identify MSV-5 paralogs with equal genotypes
locateParalogues        Match paralogs with chromosomes
makeDiploidCalls        Constrain calls to diploid representation
makeFilenames           Generate filenames reflecting normalizations
manualCall              Interactive calling of genotype for single
                        marker
normalizeShearedChannels
                        Channel normalization
plotGenotypes           Plotting of genotyped markers
preprocessBeadSet       Pre-processing of BeadSetIllumina objects
readBeadSummaryOutput   Read bead-summary intensities from two colour
                        Illumina (Infinium) scanner
resolveInheritanceSNP   Track parental alleles in offspring
scatterArrays           Cartesian scatter-plots of two-colour
                        intensities
shearRawSignal          Affine transformation of axes
testHardyWeinberg       Test for Hardy-Weinberg equilibrium
transformChannels       Signal transformation
translateTheta          Convert genotype calls to allele information
unmixParalogues         Partially resolve the paralogs of MSV-5s
validateCallsPedigree   Pedigree validation of genotypes
writeAlleleSet          Write AlleleSetIllumina data to files
