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 |