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.

Author
Lars Gidskehaug
Date of publication
2011-02-21 06:44:19
Maintainer
Lars Gidskehaug <lg@camo.no>
License
GPL (>= 2)
Version
1.1.0

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

Files in this package

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