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.

Functions

ABpanel Man page
BafLrrSetList Man page
BafLrrSetList,CNSet-method Man page
CA Man page
CA,CNSet-method Man page
calculateRBaf Man page
calculateRBaf,CNSet-method Man page
CB Man page
CB,CNSet-method Man page
celDates Man page
cnrmaAffy Man page
cnSetExample Man page
cnSetExample2 Man page
coerce,CNSet,oligoSnpSet-method Man page
constructAffyCNSet Man page
constructInf Man page
corr Man page
corr,AssayData-method Man page
corr,CNSet-method Man page
crlmm Man page
crlmm2 Man page
crlmmCopynumber Man page
crlmmCopynumber2 Man page
crlmmCopynumberLD Man page
crlmmIllumina Man page
crlmm-package Man page
genotype Man page
genotype2 Man page
genotypeAffy Man page
genotype.Illumina Man page
genotypeInf Man page
genotypeLD Man page
genotypes Man page
lines,CNSet-method Man page
mads Man page
mads,AssayData-method Man page
mads,CNSet-method Man page
medians Man page
medians,AssayData-method Man page
medians,CNSet-method Man page
Ns Man page
Ns,AssayData-method Man page
Ns,CNSet-method Man page
nuA Man page
nuA,CNSet-method Man page
nuB Man page
nuB,CNSet-method Man page
OligoSetList Man page
OligoSetList,CNSet-method Man page
phiA Man page
phiA,CNSet-method Man page
phiB Man page
phiB,CNSet-method Man page
plotSamples Man page
plotSNPs Man page
posteriorProbability Man page
posteriorProbability,CNSet-method Man page
predictionRegion Man page
[,PredictionRegion,ANY,ANY,ANY-method Man page
PredictionRegion-class Man page
predictionRegion,CNSet,integer-method Man page
preprocessInf Man page
rawCopynumber Man page
rawCopynumber,CNSet-method Man page
readGenCallOutput Man page
readIdatFiles Man page
readIdatFiles2 Man page
snprma Man page
snprma2 Man page
snprmaAffy Man page
tau2 Man page
tau2,AssayData-method Man page
tau2,CNSet-method Man page
totalCopynumber Man page
totalCopynumber,CNSet-method Man page
validCdfNames Man page
validCEL Man page
xyplot Man page
xyplot,formula,CNSet-method Man page

Files

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

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

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