Package: crlmm 1.70.0

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_1.70.0.tar.gz
crlmm_1.70.0.zip(r-4.7)crlmm_1.70.0.zip(r-4.6)crlmm_1.70.0.zip(r-4.5)
crlmm_1.70.0.tgz(r-4.6-x86_64)crlmm_1.70.0.tgz(r-4.6-arm64)crlmm_1.70.0.tgz(r-4.5-x86_64)crlmm_1.70.0.tgz(r-4.5-arm64)
crlmm_1.70.0.tar.gz(r-4.7-arm64)crlmm_1.70.0.tar.gz(r-4.7-x86_64)crlmm_1.70.0.tar.gz(r-4.6-arm64)crlmm_1.70.0.tar.gz(r-4.6-x86_64)
crlmm_1.70.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
crlmm/json (API)
NEWS

# Install 'crlmm' in R:

install.packages('crlmm', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

cnSetExample - Object of class 'CNSet'
cnSetExample2 - Object of class 'CNSet'

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.

microarray preprocessing snp copynumbervariation

6.39 score 3 packages 38 scripts 687 downloads 6 mentions 46 exports 55 dependencies

Last updated from:416d6f5231 (on RELEASE_3_23). Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: no.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	223
linux-devel-arm64	WARNING	524
linux-devel-x86_64	WARNING	593
source / vignettes	OK	262
linux-release-arm64	WARNING	467
linux-release-x86_64	WARNING	551
macos-release-arm64	WARNING	517
macos-release-x86_64	WARNING	636
macos-oldrel-arm64	WARNING	487
macos-oldrel-x86_64	WARNING	1051
windows-devel	WARNING	582
windows-release	WARNING	340
windows-oldrel	WARNING	629
wasm-release	OK	196

Exports:A ABpanel B BafLrrSetList CA calculateRBaf CB celDates cnrmaAffy constructAffyCNSet corr crlmm crlmm2 crlmmCopynumber crlmmCopynumber2 crlmmCopynumberLD crlmmIllumina genotype genotype.Illumina genotype2 genotypeAffy genotypeLD genotypes mads medians Ns nuA nuB OligoSetList phiA phiB plotSamples plotSNPs posteriorProbability predictionRegion rawCopynumber readGenCallOutput readIdatFiles snprma snprma2 snprmaAffy tau2 totalCopynumber validCdfNames validCEL xyplot

Dependencies:abind affyio askpass base64 beanplot Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli codetools cpp11 crayon DBI DelayedArray ellipse fastmap ff foreach generics GenomicRanges glue illuminaio IRanges iterators lattice lifecycle limma Matrix MatrixGenerics matrixStats memoise mvtnorm oligoClasses openssl pkgconfig preprocessCore Rcpp RcppEigen rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray statmod SummarizedExperiment sys vctrs VGAM XVector

Copy number estimation

Rendered fromAffyGW.Rnwusingutils::Sweaveon Jun 04 2026.

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

crlmm Vignette - Downstream Analysis

Rendered fromgtypeDownstream.Rnwusingutils::Sweaveon Jun 04 2026.

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

crlmm Vignette - Genotyping

Rendered fromgenotyping.Rnwusingutils::Sweaveon Jun 04 2026.

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

Infrastructure for copy number analysis

Rendered fromInfrastructure.Rnwusingutils::Sweaveon Jun 04 2026.

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

Overview of copy number vignettes

Rendered fromCopyNumberOverview.Rnwusingutils::Sweaveon Jun 04 2026.

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

Preprocessing and genotyping Illumina arrays for copy number analysis

Rendered fromIlluminaPreprocessCN.Rnwusingutils::Sweaveon Jun 04 2026.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Genotype Calling via CRLMM Algorithm	crlmm-package
A panel function for plotting prediction regions and log-normalized intensities	ABpanel
Methods for class "AssayData" in crlmm	corr,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 markers	cnrmaAffy
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 files	constructAffyCNSet
Instantiate an object of class CNSet for the Infinium platforms.	constructInf
Accessors for allele-specific or total copy number	CA CB nuA nuB phiA phiB rawCopynumber totalCopynumber
Genotype oligonucleotide arrays with CRLMM	crlmm crlmm2
Locus- and allele-specific estimation of copy number	crlmmCopynumber 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 files	genotypeAffy
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 number	predictionRegion 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 output	readGenCallOutput
Reads Idat Files from Infinium II Illumina BeadChips	readIdatFiles readIdatFiles2
Preprocessing tool for SNP arrays.	snprma snprma2
Quantile normalize intensities for SNPs	snprmaAffy
Supported annotation packages for crlmm genotyping	validCdfNames
Reads cel files and return an error if a file is not read	celDates validCEL
Plot prediction regions and normalized intensities.	xyplot xyplot,formula,CNSet-method

Usage by other packages (reverse dependencies)