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

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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.

Author
Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
Date of publication
None
Maintainer
Benilton S Carvalho <benilton@unicamp.br>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
License
Artistic-2.0
Version
1.32.0

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