Analysis of Illumina BeadArray SNP data including MSV markers


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Documentation for package ‘beadarrayMSV’ version 1.1.0

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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