crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Version 1.34.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorBenilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
Bioconductor views CopyNumberVariation Microarray Preprocessing SNP
Date of publicationNone
MaintainerBenilton S Carvalho <benilton@unicamp.br>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
LicenseArtistic-2.0
Version1.34.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("crlmm")

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 Source code
ACN Source code
AddBackNoVarianceSNPs Source code
BafLrrSetList Man page
BafLrrSetList,CNSet-method Man page
C1 Source code
C2 Source code
C3 Source code
CA Man page
CA,CNSet-method Man page
CB Man page
CB,CNSet-method Man page
Ns Man page
Ns,AssayData-method Man page
Ns,CNSet-method Man page
OligoSetList Man page
OligoSetList,CNSet-method Man page
PredictionRegion-class Man page
RGtoXY Source code
[,PredictionRegion,ANY,ANY,ANY-method Man page
affyCdfNames Source code
assignCalls Source code
assignCalls1Cluster Source code
assignCalls2Cluster Source code
assignCalls3Cluster Source code
assignCallsOneSNP Source code
calculateKrlmmCoefficients Source code
calculateMahalDist1Cluster Source code
calculateMahalDist2Cluster Source code
calculateMahalDist3Cluster Source code
calculateOneParams1Cluster Source code
calculateOneParams2Cluster Source code
calculateOneParams3Cluster Source code
calculateParameters Source code
calculateParameters1Cluster Source code
calculateParameters2Cluster Source code
calculateParameters3Cluster Source code
calculatePriorValues Source code
calculatePriorcentersC Source code
calculateRBaf Man page
calculateRBaf,CNSet-method Man page
calculateRBafCNSet Source code
calculateRTheta Source code
celDates Man page Source code
changeToCrlmmAnnotationName Source code
checkNumberOfSNPs Source code
cleancdfname Source code
close Source code
cnSetExample Man page
cnSetExample2 Man page
cnrma2 Source code
cnrmaAffy Man page Source code
coerce,CNSet,oligoSnpSet-method Man page
computeAverageLogIntensity Source code
computeCallPr Source code
computeLogRatio Source code
construct Source code
constructAffyCNSet Man page Source code
constructBafLrrSetListFrom Source code
constructIlluminaAssayData Source code
constructIlluminaCNSet Source code
constructIlluminaFeatureData Source code
constructInf Man page Source code
constructOligoSetListFrom Source code
corr Man page
corr,AssayData-method Man page
corr,CNSet-method Man page
crlmm Man page Source code
crlmm-package Man page
crlmm2 Man page Source code
crlmmCopynumber Man page Source code
crlmmCopynumber2 Man page Source code
crlmmCopynumberLD Man page
crlmmGT Source code
crlmmGT2 Source code
crlmmIllumina Man page
dbvn Source code
dqrlsWrapper Source code
ellipseCenters Source code
estimateCnParameters Source code
fit.lm1 Source code
fit.lm2 Source code
fit.lm3 Source code
fit.lm4 Source code
fit.wls Source code
fitAffySnpMixture56 Source code
genotype Man page Source code
genotype.Illumina Man page Source code
genotype2 Man page Source code
genotypeAffy Man page Source code
genotypeCorrelation Source code
genotypeInf Man page Source code
genotypeLD Man page
genotypeSummary Source code
genotypes Man page Source code
getAvailableIlluminaGenomeBuild Source code
getBAF Source code
getCor Source code
getCrlmmAnnotationName Source code
getFeatureData Source code
getKrlmmVGLMCoefficients Source code
getMedians Source code
getNumberOfCores Source code
getNumberOfSNPs Source code
getNumberOfSamples Source code
getProtocolData.Affy Source code
getProtocolData.Illumina Source code
getSigma2 Source code
getTau2 Source code
getVar Source code
getVarInEnv Source code
gtypeCallerR Source code
gtypeCallerR2 Source code
hardyweinberg Source code
illuminaCdfNames Source code
imputeAA Source code
imputeAA.AB Source code
imputeAB.BB Source code
imputeAcrossBatch Source code
imputeBB Source code
imputeCenter Source code
imputeCenterX Source code
imputeCentersForMonomorphicSnps Source code
imputeGender Source code
indexComplete Source code
intMedianSummaries Source code
isCall Source code
isLoaded Source code
isPackageLoaded Source code
isValidCdfName Source code
krlmm Source code
krlmmImputeGender Source code
krlmmnopkg Source code
linearParamElementReplace Source code
lines,CNSet-method Man page
list2SnpSet Source code
loadObject Source code
loader Source code
loessnormalization Source code
mads Man page
mads,AssayData-method Man page
mads,CNSet-method Man page
medianSummaries Source code
medians Man page
medians,AssayData-method Man page
medians,CNSet-method Man page
nuA Man page
nuA,CNSet-method Man page
nuB Man page
nuB,CNSet-method Man page
numberGenotypes Source code
onAttach Source code
onUnload Source code
open Source code
paramNames Source code
phiA Man page
phiA,CNSet-method Man page
phiB Man page
phiB,CNSet-method Man page
plotSNPs Man page Source code
plotSamples Man page Source code
posterior Source code
posteriorMean.snp Source code
posteriorProbability Man page
posteriorProbability,CNSet-method Man page
predictKwithVGLM Source code
predictionRegion Man page
predictionRegion,CNSet,integer-method Man page
preprocessInf Man page Source code
preprocessInfinium2 Source code
processCEL Source code
processIDAT Source code
processOneGenCallFile Source code
quantilenormalization Source code
rawCopynumber Man page
rawCopynumber,CNSet-method Man page
readGenCallOutput Man page Source code
readIdatFiles Man page Source code
readIdatFiles2 Man page
rowCors Source code
rowCovs Source code
rowMAD Source code
shrink Source code
shrinkGenotypeSummaries Source code
shrinkSummary Source code
snprma Man page Source code
snprma2 Man page Source code
snprmaAffy Man page Source code
stripNormalize Source code
stupidSplineBasis Source code
sum.mymatrix Source code
summarizeMaleXNps Source code
summarizeNps Source code
summarizeSnps Source code
summarizeXGenotypes Source code
tau2 Man page
tau2,AssayData-method Man page
tau2,CNSet-method Man page
test Source code
totalCopynumber Man page
totalCopynumber,CNSet-method Man page
validCEL Man page Source code
validCdfNames Man page Source code
verifyChrXSNPs Source code
verifyChrYSNPs Source code
whichMarkers Source code
whichPlatform Source code
xyplot Man page
xyplot,formula,CNSet-method Man page

Files

.Rinstignore
CHANGES
DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/cnrma-functions.R
R/cnset-accessors.R
R/crlmm-functions.R
R/crlmm-illumina.R
R/crlmmGT2.R
R/krlmm.R
R/methods-AssayData.R
R/methods-CNSet.R
R/methods-CNSetLM.R
R/methods-PredictionRegion.R
R/methods-SnpSuperSet.R
R/methods-eSet.R
R/plot.R
R/snprma-functions.R
R/test_crlmm_package.R
R/utils.R
R/zzz.R
TODO
build
build/vignette.rds
data
data/cnSetExample.rda
data/cnSetExample2.rda
data/datalist
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/AffyGW.Rnw
inst/doc/AffyGW.pdf
inst/doc/CopyNumberOverview.Rnw
inst/doc/CopyNumberOverview.pdf
inst/doc/IlluminaPreprocessCN.Rnw
inst/doc/IlluminaPreprocessCN.pdf
inst/doc/Infrastructure.Rnw
inst/doc/Infrastructure.pdf
inst/doc/genotyping.R
inst/doc/genotyping.Rnw
inst/doc/genotyping.pdf
inst/doc/gtypeDownstream.Rnw
inst/doc/gtypeDownstream.pdf
inst/scripts
inst/scripts/AffyGW.Rnw
inst/scripts/AffyGW.pdf
inst/scripts/IlluminaPreprocessCN.Rnw
inst/scripts/IlluminaPreprocessCN.pdf
inst/scripts/Infrastructure.Rnw
inst/scripts/Infrastructure.pdf
inst/scripts/Makefile
inst/scripts/copynumber.Rnw
inst/scripts/crlmmDownstream.pdf
inst/scripts/crlmmIllumina.Rnw
inst/scripts/crlmmIllumina.pdf
inst/scripts/gtypeDownstream.Rnw
inst/scripts/gtypeDownstream.pdf
inst/scripts/refs.bib
inst/scripts/sync
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/test_crlmm.R
inst/unitTests/test_dataExamples.R
inst/unitTests/test_ff.R
man
man/ABpanel.Rd
man/AssayData-methods.Rd
man/CNSet-methods.Rd
man/ListClassConstructors.Rd
man/PredictionRegion-class.Rd
man/batchStatisticAccessors.Rd
man/calculateRBaf.Rd
man/celfile-utils.Rd
man/cnSetExample.Rd
man/cnrmaAffy.Rd
man/constructAffyCNSet.Rd
man/constructInf.Rd
man/copynumberAccessors.Rd
man/crlmm-package.Rd
man/crlmm.Rd
man/crlmmCopynumber.Rd
man/genotype.Illumina.Rd
man/genotype.Rd
man/genotypeAffy.Rd
man/genotypeInf.Rd
man/genotypes.Rd
man/plotSNPs.Rd
man/posteriorProbability.Rd
man/predictionRegion.Rd
man/preprocessInf.Rd
man/readGenCallOutput.Rd
man/readIdatFiles.Rd
man/snprma.Rd
man/snprmaAffy.Rd
man/validCdfNames.Rd
man/xyplot.Rd
src
src/crlmm.h
src/gtypeCaller.c
src/init.c
src/trimmed.c
src/utils.c
src/utils.h
tests
tests/crlmm_unit_tests.R
tests/doRUnit.R
vignettes
vignettes/AffyGW.Rnw
vignettes/CopyNumberOverview.Rnw
vignettes/IlluminaPreprocessCN.Rnw
vignettes/Infrastructure.Rnw
vignettes/Makefile
vignettes/crlmmIllumina.pdf
vignettes/genotyping.Rnw
vignettes/gtypeDownstream.Rnw
crlmm documentation built on May 20, 2017, 10:54 p.m.