Package: crlmm 1.65.0

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

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crlmm.pdf |crlmm.html✨
crlmm/json (API)
NEWS

# Install 'crlmm' in R:

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

Datasets:

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

On BioConductor:crlmm-1.65.0(bioc 3.21)crlmm-1.64.0(bioc 3.20)

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

microarray preprocessing snp copynumbervariation

4.60 score 3 packages 37 scripts 532 downloads 6 mentions 46 exports 63 dependencies

Last updated 23 days agofrom:de849d9769. Checks:ERROR: 2 WARNING: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Oct 31 2024
R-4.5-win-x86_64	WARNING	Oct 31 2024
R-4.5-linux-x86_64	ERROR	Oct 31 2024
R-4.4-win-x86_64	WARNING	Oct 31 2024
R-4.4-mac-x86_64	WARNING	Oct 31 2024
R-4.4-mac-aarch64	WARNING	Oct 31 2024
R-4.3-win-x86_64	WARNING	Oct 31 2024
R-4.3-mac-x86_64	WARNING	Oct 31 2024
R-4.3-mac-aarch64	WARNING	Oct 31 2024

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 curl DBI DelayedArray ellipse fastmap ff foreach GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr illuminaio IRanges iterators jsonlite lattice lifecycle limma Matrix MatrixGenerics matrixStats memoise mime mvtnorm oligoClasses openssl pkgconfig plogr preprocessCore R6 Rcpp RcppEigen rlang RSQLite S4Arrays S4Vectors SparseArray statmod SummarizedExperiment sys UCSC.utils vctrs VGAM XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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