# Analysis of Illumina BeadArray SNP data including MSV markers

## Documentation for package ‘beadarrayMSV’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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