Man pages for beadarrayMSV
Analysis of Illumina BeadArray SNP data including MSV markers

AlleleSetIllumina-classClass to Contain Objects Describing High-Throughput Illumina...
assignParaloguesAssign MSV-5 paralogs to chromosomes
beadarrayMSV-packagebeadarrayMSV: Package for analysis of high-throughput...
BeadSetIllumina-classClass to Contain Objects Describing High-Throughput Illumina...
BSRed.193Atlantic salmon genotype data with mainly MSV-5 markers
callGenotypesClustering and calling of genotypes
cart2polTransformation from Cartesian to polar coordinates
countFailedSNPCalculate ratio of called markers for each array
createAlleleSetCreate AlleleSetIllumina or MultiSet objects
findClustersSuggest clusters based on histograms
findPolyploidClustersK-means clustering
findSeThetaScale pooled standard errors after polar transformation
generatePolyCentersGenerate list of possible genotype categories
getCentersEstimate starting points for clustering
getNoiseDistributionsEstimate median and robust spread of background noise
getNormIndRetrieve sub-bead pool indexes
getSingleCallsIdentify MSV-5 paralogs with equal genotypes
locateParaloguesMatch paralogs with chromosomes
makeDiploidCallsConstrain calls to diploid representation
makeFilenamesGenerate filenames reflecting normalizations
manualCallInteractive calling of genotype for single marker
normalizeShearedChannelsChannel normalization
plotGenotypesPlotting of genotyped markers
preprocessBeadSetPre-processing of BeadSetIllumina objects
readBeadSummaryOutputRead bead-summary intensities from two colour Illumina...
resolveInheritanceSNPTrack parental alleles in offspring
scatterArraysCartesian scatter-plots of two-colour intensities
shearRawSignalAffine transformation of axes
testHardyWeinbergTest for Hardy-Weinberg equilibrium
transformChannelsSignal transformation
translateThetaConvert genotype calls to allele information
unmixParaloguesPartially resolve the paralogs of MSV-5s
validateCallsPedigreePedigree validation of genotypes
writeAlleleSetWrite AlleleSetIllumina data to files
beadarrayMSV documentation built on May 1, 2019, 6:33 p.m.