beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Imports bead-summary data from Illumina scanner. Pre-processes using a suite of optional normalizations and transformations. Clusters and automatically calls genotypes, critically able to handle markers in duplicated regions of the genome (multisite variants; MSVs). Interactive clustering if needed. MSVs with variation in both paralogs may be resolved and mapped to their respective chromosomes. Quality control including pedigree checking and visual assessment of clusters. Too large data-sets are handled by working on smaller subsets of the data in sequence.

AuthorLars Gidskehaug
Date of publication2011-02-21 06:44:19
MaintainerLars Gidskehaug <lg@camo.no>
LicenseGPL (>= 2)
Version1.1.0

View on CRAN

Man pages

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

Functions

AlleleSetIllumina-class Man page
assignParalogues Man page
assignToAlleleSet Man page
beadarrayMSV Man page
beadarrayMSV-package Man page
BeadSetIllumina-class Man page
BSRed.193 Man page
callGenotypes Man page
callGenotypes.interactive Man page
callGenotypes.verboseTest Man page
cart2pol Man page
countFailedSNP Man page
createAlleleSet Man page
createAlleleSetFromFiles Man page
createMultiSetFromFiles Man page
findClusters Man page
findPolyploidClusters Man page
findSeTheta Man page
generatePolyCenters Man page
getCenters Man page
getNoiseDistributions Man page
getNormInd Man page
getSingleCalls Man page
getSpecificCenters Man page
initialize,AlleleSetIllumina-method Man page
initialize,BeadSetIllumina-method Man page
locateParalogues Man page
makeDiploidCalls Man page
makeFilenames Man page
manualCall Man page
modifyExistingFilenames Man page
normalizeIllumina Man page
normalizeShearedChannels Man page
plotCountsChrom Man page
plotEstimatedNoise Man page
plotGenotypes Man page
plotPreprocessing Man page
preprocessBeadSet Man page
readBeadSummaryOutput Man page
resolveInheritanceSNP Man page
scatterArrays Man page
setGenoOptions Man page
setMergeOptions Man page
setNormOptions Man page
shearRawSignal Man page
testHardyWeinberg Man page
transformChannels Man page
transformSEs Man page
translateTheta Man page
translateThetaCombined Man page
translateThetaFromFiles Man page
unmixParalogues Man page
validateCallsPedigree Man page
validateSingleCall Man page
writeAlleleSet Man page

Files

beadarrayMSV
beadarrayMSV/NAMESPACE
beadarrayMSV/inst
beadarrayMSV/inst/CITATION
beadarrayMSV/inst/ChangeLog
beadarrayMSV/inst/extdata
beadarrayMSV/inst/extdata/sampleData.txt
beadarrayMSV/inst/extdata/Theta_root_medianAF_testdata.txt
beadarrayMSV/inst/extdata/4469076125
beadarrayMSV/inst/extdata/4469076125/4469076125_A_beadTypeFile.txt
beadarrayMSV/inst/extdata/4469076125/4469076125_B_beadTypeFile.txt
beadarrayMSV/inst/extdata/4469076309
beadarrayMSV/inst/extdata/4469076309/4469076309_A_beadTypeFile.txt
beadarrayMSV/inst/extdata/4469076309/4469076309_B_beadTypeFile.txt
beadarrayMSV/inst/extdata/beadData.txt
beadarrayMSV/inst/extdata/SE_root_medianAF_testdata.txt
beadarrayMSV/inst/extdata/beadData_testdata.txt
beadarrayMSV/inst/extdata/Pheno_root_medianAF_testdata.txt
beadarrayMSV/inst/extdata/Int_root_medianAF_testdata.txt
beadarrayMSV/inst/doc
beadarrayMSV/inst/doc/cookbookBeadarrayMSV.pdf
beadarrayMSV/data
beadarrayMSV/data/datalist
beadarrayMSV/data/BSRed.193.RData
beadarrayMSV/DESCRIPTION
beadarrayMSV/man
beadarrayMSV/man/BeadSetIllumina-class.Rd beadarrayMSV/man/findPolyploidClusters.Rd beadarrayMSV/man/unmixParalogues.Rd beadarrayMSV/man/scatterArrays.Rd beadarrayMSV/man/beadarrayMSV-package.Rd beadarrayMSV/man/shearRawSignal.Rd beadarrayMSV/man/translateTheta.Rd beadarrayMSV/man/createAlleleSet.Rd beadarrayMSV/man/readBeadSummaryOutput.Rd beadarrayMSV/man/getNoiseDistributions.Rd beadarrayMSV/man/plotGenotypes.Rd beadarrayMSV/man/cart2pol.Rd beadarrayMSV/man/assignParalogues.Rd beadarrayMSV/man/BSRed.193.Rd beadarrayMSV/man/locateParalogues.Rd beadarrayMSV/man/generatePolyCenters.Rd beadarrayMSV/man/getSingleCalls.Rd beadarrayMSV/man/testHardyWeinberg.Rd beadarrayMSV/man/normalizeShearedChannels.Rd beadarrayMSV/man/preprocessBeadSet.Rd beadarrayMSV/man/makeDiploidCalls.Rd beadarrayMSV/man/findSeTheta.Rd beadarrayMSV/man/validateCallsPedigree.Rd beadarrayMSV/man/manualCall.Rd beadarrayMSV/man/findClusters.Rd beadarrayMSV/man/callGenotypes.Rd beadarrayMSV/man/getCenters.Rd beadarrayMSV/man/AlleleSetIllumina-class.Rd beadarrayMSV/man/makeFilenames.Rd beadarrayMSV/man/countFailedSNP.Rd beadarrayMSV/man/resolveInheritanceSNP.Rd beadarrayMSV/man/writeAlleleSet.Rd beadarrayMSV/man/transformChannels.Rd beadarrayMSV/man/getNormInd.Rd
beadarrayMSV/R
beadarrayMSV/R/beadarrayMSV.R

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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