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| beadarrayMSV-package | beadarrayMSV: Package for analysis of high-throughput Illumina BeadArrays |
| AlleleSetIllumina-class | Class to Contain Objects Describing High-Throughput Illumina BeadArrays |
| assignParalogues | Assign MSV-5 paralogs to chromosomes |
| assignToAlleleSet | Create AlleleSetIllumina or MultiSet objects |
| beadarrayMSV | beadarrayMSV: Package for analysis of high-throughput Illumina BeadArrays |
| BeadSetIllumina-class | Class to Contain Objects Describing High-Throughput Illumina BeadArrays |
| BSRed.193 | Atlantic salmon genotype data with mainly MSV-5 markers |
| callGenotypes | Clustering and calling of genotypes |
| callGenotypes.interactive | Clustering and calling of genotypes |
| callGenotypes.verboseTest | 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 |
| createAlleleSetFromFiles | Create AlleleSetIllumina or MultiSet objects |
| createMultiSetFromFiles | 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 |
| getSpecificCenters | Estimate starting points for clustering |
| initialize-method | Class to Contain Objects Describing High-Throughput Illumina BeadArrays |
| initialize-method | Class to Contain Objects Describing High-Throughput Illumina BeadArrays |
| locateParalogues | Match paralogs with chromosomes |
| makeDiploidCalls | Constrain calls to diploid representation |
| makeFilenames | Generate filenames reflecting normalizations |
| manualCall | Interactive calling of genotype for single marker |
| modifyExistingFilenames | Generate filenames reflecting normalizations |
| normalizeIllumina | Affine transformation of axes |
| normalizeShearedChannels | Channel normalization |
| plotCountsChrom | Match paralogs with chromosomes |
| plotEstimatedNoise | Estimate median and robust spread of background noise |
| plotGenotypes | Plotting of genotyped markers |
| plotPreprocessing | Pre-processing of BeadSetIllumina objects |
| 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 |
| setGenoOptions | Clustering and calling of genotypes |
| setMergeOptions | Assign MSV-5 paralogs to chromosomes |
| setNormOptions | Pre-processing of BeadSetIllumina objects |
| shearRawSignal | Affine transformation of axes |
| testHardyWeinberg | Test for Hardy-Weinberg equilibrium |
| transformChannels | Signal transformation |
| transformSEs | Signal transformation |
| translateTheta | Convert genotype calls to allele information |
| translateThetaCombined | Convert genotype calls to allele information |
| translateThetaFromFiles | Convert genotype calls to allele information |
| unmixParalogues | Partially resolve the paralogs of MSV-5s |
| validateCallsPedigree | Pedigree validation of genotypes |
| validateSingleCall | Pedigree validation of genotypes |
| writeAlleleSet | Write AlleleSetIllumina data to files |