crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.

AuthorBenilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
Date of publicationNone
MaintainerBenilton S Carvalho <benilton@unicamp.br>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
LicenseArtistic-2.0
Version1.32.0

View on Bioconductor

Man pages

ABpanel: A panel function for plotting prediction regions and...

AssayData-methods: Methods for class "AssayData" in crlmm

batchStatisticAccessors: Accessors for batch-specific summary statistics.

calculateRBaf: Calculate log R ratios and B allele frequencies.

celfile-utils: Reads cel files and return an error if a file is not read

cnrmaAffy: quantile normalize nonpolymorphic markers

cnSetExample: Object of class 'CNSet'

CNSet-methods: crlmm methods for class "CNSet"

constructAffyCNSet: Construct an object of class CNSet from Affymetrix cel files

constructInf: Instantiate an object of class CNSet for the Infinium...

copynumberAccessors: Accessors for allele-specific or total copy number

crlmm: Genotype oligonucleotide arrays with CRLMM

crlmmCopynumber: Locus- and allele-specific estimation of copy number

crlmm-package: Genotype Calling via CRLMM Algorithm

genotype: Preprocessing and genotyping of Affymetrix arrays.

genotypeAffy: Genotype Affymetrix CEL files

genotype.Illumina: Preprocessing and genotyping of Illumina Infinium II arrays.

genotypeInf: Genotyping of Illumina Infinium II arrays.

genotypes: The possible genotypes for an integer copy number.

ListClassConstructors: Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~

plotSNPs: Make M vs S plot for SNPs or samples.

posteriorProbability: Calculate the posterior probability for integer copy numbers.

predictionRegion: Prediction regions for integer copy number

PredictionRegion-class: Class '"PredictionRegion"'

preprocessInf: Preprocessing of Illumina Infinium II arrays.

readGenCallOutput: Read X and Y intensities from GenCall output

readIdatFiles: Reads Idat Files from Infinium II Illumina BeadChips

snprma: Preprocessing tool for SNP arrays.

snprmaAffy: Quantile normalize intensities for SNPs

validCdfNames: Supported annotation packages for crlmm genotyping

xyplot: Plot prediction regions and normalized intensities.

Files in this package

crlmm/.Rinstignore
crlmm/CHANGES
crlmm/DESCRIPTION
crlmm/NAMESPACE
crlmm/R
crlmm/R/AllClasses.R crlmm/R/AllGenerics.R crlmm/R/cnrma-functions.R crlmm/R/cnset-accessors.R crlmm/R/crlmm-functions.R crlmm/R/crlmm-illumina.R crlmm/R/crlmmGT2.R crlmm/R/krlmm.R crlmm/R/methods-AssayData.R crlmm/R/methods-CNSet.R crlmm/R/methods-CNSetLM.R crlmm/R/methods-PredictionRegion.R crlmm/R/methods-SnpSuperSet.R crlmm/R/methods-eSet.R crlmm/R/plot.R crlmm/R/snprma-functions.R crlmm/R/test_crlmm_package.R crlmm/R/utils.R crlmm/R/zzz.R
crlmm/TODO
crlmm/build
crlmm/build/vignette.rds
crlmm/data
crlmm/data/cnSetExample.rda
crlmm/data/cnSetExample2.rda
crlmm/data/datalist
crlmm/inst
crlmm/inst/CITATION
crlmm/inst/NEWS.Rd
crlmm/inst/doc
crlmm/inst/doc/AffyGW.Rnw
crlmm/inst/doc/AffyGW.pdf
crlmm/inst/doc/CopyNumberOverview.Rnw
crlmm/inst/doc/CopyNumberOverview.pdf
crlmm/inst/doc/IlluminaPreprocessCN.Rnw
crlmm/inst/doc/IlluminaPreprocessCN.pdf
crlmm/inst/doc/Infrastructure.Rnw
crlmm/inst/doc/Infrastructure.pdf
crlmm/inst/doc/genotyping.R
crlmm/inst/doc/genotyping.Rnw
crlmm/inst/doc/genotyping.pdf
crlmm/inst/doc/gtypeDownstream.Rnw
crlmm/inst/doc/gtypeDownstream.pdf
crlmm/inst/scripts
crlmm/inst/scripts/AffyGW.Rnw
crlmm/inst/scripts/AffyGW.pdf
crlmm/inst/scripts/IlluminaPreprocessCN.Rnw
crlmm/inst/scripts/IlluminaPreprocessCN.pdf
crlmm/inst/scripts/Infrastructure.Rnw
crlmm/inst/scripts/Infrastructure.pdf
crlmm/inst/scripts/Makefile
crlmm/inst/scripts/copynumber.Rnw
crlmm/inst/scripts/crlmmDownstream.pdf
crlmm/inst/scripts/crlmmIllumina.Rnw
crlmm/inst/scripts/crlmmIllumina.pdf
crlmm/inst/scripts/gtypeDownstream.Rnw
crlmm/inst/scripts/gtypeDownstream.pdf
crlmm/inst/scripts/refs.bib
crlmm/inst/scripts/sync
crlmm/inst/unitTests
crlmm/inst/unitTests/Makefile
crlmm/inst/unitTests/test_crlmm.R
crlmm/inst/unitTests/test_dataExamples.R
crlmm/inst/unitTests/test_ff.R
crlmm/man
crlmm/man/ABpanel.Rd crlmm/man/AssayData-methods.Rd crlmm/man/CNSet-methods.Rd crlmm/man/ListClassConstructors.Rd crlmm/man/PredictionRegion-class.Rd crlmm/man/batchStatisticAccessors.Rd crlmm/man/calculateRBaf.Rd crlmm/man/celfile-utils.Rd crlmm/man/cnSetExample.Rd crlmm/man/cnrmaAffy.Rd crlmm/man/constructAffyCNSet.Rd crlmm/man/constructInf.Rd crlmm/man/copynumberAccessors.Rd crlmm/man/crlmm-package.Rd crlmm/man/crlmm.Rd crlmm/man/crlmmCopynumber.Rd crlmm/man/genotype.Illumina.Rd crlmm/man/genotype.Rd crlmm/man/genotypeAffy.Rd crlmm/man/genotypeInf.Rd crlmm/man/genotypes.Rd crlmm/man/plotSNPs.Rd crlmm/man/posteriorProbability.Rd crlmm/man/predictionRegion.Rd crlmm/man/preprocessInf.Rd crlmm/man/readGenCallOutput.Rd crlmm/man/readIdatFiles.Rd crlmm/man/snprma.Rd crlmm/man/snprmaAffy.Rd crlmm/man/validCdfNames.Rd crlmm/man/xyplot.Rd
crlmm/src
crlmm/src/crlmm.h
crlmm/src/gtypeCaller.c
crlmm/src/init.c
crlmm/src/trimmed.c
crlmm/src/utils.c
crlmm/src/utils.h
crlmm/tests
crlmm/tests/crlmm_unit_tests.R
crlmm/tests/doRUnit.R
crlmm/vignettes
crlmm/vignettes/AffyGW.Rnw
crlmm/vignettes/CopyNumberOverview.Rnw
crlmm/vignettes/IlluminaPreprocessCN.Rnw
crlmm/vignettes/Infrastructure.Rnw
crlmm/vignettes/Makefile
crlmm/vignettes/crlmmIllumina.pdf
crlmm/vignettes/genotyping.Rnw
crlmm/vignettes/gtypeDownstream.Rnw

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