AlleleSetIllumina-class | Class to Contain Objects Describing High-Throughput Illumina... |
assignParalogues | Assign MSV-5 paralogs to chromosomes |
beadarrayMSV-package | beadarrayMSV: Package for analysis of high-throughput... |
BeadSetIllumina-class | Class to Contain Objects Describing High-Throughput Illumina... |
BSRed.193 | Atlantic salmon genotype data with mainly MSV-5 markers |
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... |
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 |
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