Package: crlmm 1.71.0

Benilton S Carvalho

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.

Authors:Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry

crlmm_1.71.0.tar.gz
crlmm_1.71.0.zip(r-4.7)crlmm_1.71.0.zip(r-4.6)crlmm_1.71.0.zip(r-4.5)
crlmm_1.71.0.tgz(r-4.6-x86_64)crlmm_1.71.0.tgz(r-4.6-arm64)crlmm_1.71.0.tgz(r-4.5-x86_64)crlmm_1.71.0.tgz(r-4.5-arm64)
crlmm_1.71.0.tar.gz(r-4.7-arm64)crlmm_1.71.0.tar.gz(r-4.7-x86_64)crlmm_1.71.0.tar.gz(r-4.6-arm64)crlmm_1.71.0.tar.gz(r-4.6-x86_64)
crlmm_1.71.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
crlmm/json (API)

# Install 'crlmm' in R:
install.packages('crlmm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:crlmm-1.71.0(bioc 3.24)crlmm-1.70.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarraypreprocessingsnpcopynumbervariation

6.39 score 3 packages 38 scripts 6 mentions 46 exports 55 dependencies

Last updated from:be2bee8305. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR227
linux-devel-arm64WARNING462
linux-devel-x86_64WARNING571
source / vignettesOK300
linux-release-arm64WARNING465
linux-release-x86_64WARNING577
macos-release-arm64WARNING436
macos-release-x86_64WARNING865
macos-oldrel-arm64WARNING433
macos-oldrel-x86_64WARNING862
windows-develWARNING528
windows-releaseWARNING480
windows-oldrelWARNING516
wasm-releaseOK297

Exports:AABpanelBBafLrrSetListCAcalculateRBafCBcelDatescnrmaAffyconstructAffyCNSetcorrcrlmmcrlmm2crlmmCopynumbercrlmmCopynumber2crlmmCopynumberLDcrlmmIlluminagenotypegenotype.Illuminagenotype2genotypeAffygenotypeLDgenotypesmadsmediansNsnuAnuBOligoSetListphiAphiBplotSamplesplotSNPsposteriorProbabilitypredictionRegionrawCopynumberreadGenCallOutputreadIdatFilessnprmasnprma2snprmaAffytau2totalCopynumbervalidCdfNamesvalidCELxyplot

Dependencies:abindaffyioaskpassbase64beanplotBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicodetoolscpp11crayonDBIDelayedArrayellipsefastmapffforeachgenericsGenomicRangesglueilluminaioIRangesiteratorslatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemvtnormoligoClassesopensslpkgconfigpreprocessCoreRcppRcppEigenrlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystatmodSummarizedExperimentsysvctrsVGAMXVector

Overview of copy number vignettes
Rendered fromCopyNumberOverview.Rnwusingutils::Sweave

Last update: 2012-11-19
Started: 2012-03-23

Copy number estimation
Rendered fromAffyGW.Rnwusingutils::Sweave

Last update: 2012-03-23
Started: 2012-03-23

crlmm Vignette - Downstream Analysis
Rendered fromgtypeDownstream.Rnwusingutils::Sweave

Last update: 2012-03-23
Started: 2012-03-23

crlmm Vignette - Genotyping
Rendered fromgenotyping.Rnwusingutils::Sweave

Last update: 2012-03-23
Started: 2012-03-23

Infrastructure for copy number analysis
Rendered fromInfrastructure.Rnwusingutils::Sweave

Last update: 2012-03-23
Started: 2012-03-23

Preprocessing and genotyping Illumina arrays for copy number analysis
Rendered fromIlluminaPreprocessCN.Rnwusingutils::Sweave

Last update: 2012-03-23
Started: 2012-03-23

Readme and manuals

Help Manual

Help pageTopics
Genotype Calling via CRLMM Algorithmcrlmm-package
A panel function for plotting prediction regions and log-normalized intensitiesABpanel
Methods for class "AssayData" in crlmmcorr,AssayData-method mads,AssayData-method medians,AssayData-method Ns,AssayData-method tau2,AssayData-method
Accessors for batch-specific summary statistics.corr mads medians Ns tau2
Calculate log R ratios and B allele frequencies.calculateRBaf calculateRBaf,CNSet-method
quantile normalize nonpolymorphic markerscnrmaAffy
crlmm methods for class "CNSet"BafLrrSetList,CNSet-method CA,CNSet-method CB,CNSet-method coerce,CNSet,oligoSnpSet-method corr,CNSet-method lines,CNSet-method mads,CNSet-method medians,CNSet-method Ns,CNSet-method nuA,CNSet-method nuB,CNSet-method OligoSetList,CNSet-method phiA,CNSet-method phiB,CNSet-method rawCopynumber,CNSet-method tau2,CNSet-method totalCopynumber,CNSet-method
Object of class 'CNSet'cnSetExample cnSetExample2
Construct an object of class CNSet from Affymetrix cel filesconstructAffyCNSet
Instantiate an object of class CNSet for the Infinium platforms.constructInf
Accessors for allele-specific or total copy numberCA CB nuA nuB phiA phiB rawCopynumber totalCopynumber
Genotype oligonucleotide arrays with CRLMMcrlmm crlmm2
Locus- and allele-specific estimation of copy numbercrlmmCopynumber crlmmCopynumber2 crlmmCopynumberLD
Preprocessing and genotyping of Affymetrix arrays.genotype genotype2 genotypeLD
Preprocessing and genotyping of Illumina Infinium II arrays.crlmmIllumina genotype.Illumina
Genotype Affymetrix CEL filesgenotypeAffy
Genotyping of Illumina Infinium II arrays.genotypeInf
The possible genotypes for an integer copy number.genotypes
Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~BafLrrSetList OligoSetList
Make M vs S plot for SNPs or samples.plotSamples plotSNPs
Calculate the posterior probability for integer copy numbers.posteriorProbability posteriorProbability,CNSet-method
Prediction regions for integer copy numberpredictionRegion predictionRegion,CNSet,integer-method
Class '"PredictionRegion"'PredictionRegion-class [,PredictionRegion,ANY,ANY,ANY-method
Preprocessing of Illumina Infinium II arrays.preprocessInf
Read X and Y intensities from GenCall outputreadGenCallOutput
Reads Idat Files from Infinium II Illumina BeadChipsreadIdatFiles readIdatFiles2
Preprocessing tool for SNP arrays.snprma snprma2
Quantile normalize intensities for SNPssnprmaAffy
Supported annotation packages for crlmm genotypingvalidCdfNames
Reads cel files and return an error if a file is not readcelDates validCEL
Plot prediction regions and normalized intensities.xyplot xyplot,formula,CNSet-method