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Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

Bioconductor version: Release (3.2)

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

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

Maintainer: Benilton S Carvalho <Benilton.Carvalho at>, Robert Scharpf <rscharpf at>, Matt Ritchie <mritchie at wehi.EDU.AU>

Citation (from within R, enter citation("crlmm")):


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PDF Copy number estimation
PDF crlmm Vignette - Downstream Analysis
PDF crlmm Vignette - Genotyping
PDF Infrastructure for copy number analysis
PDF Overview of copy number vignettes
PDF Preprocessing and genotyping Illumina arrays for copy number analysis
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version 1.28.0
In Bioconductor since BioC 2.4 (R-2.9) (6.5 years)
License Artistic-2.0
Depends R (>= 2.14.0), oligoClasses(>= 1.21.12), preprocessCore(>= 1.17.7)
Imports methods, Biobase(>= 2.15.4), BiocGenerics, affyio(>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip, utils, lattice, ff, foreach, RcppEigen (>=, matrixStats, VGAM, parallel
LinkingTo preprocessCore(>= 1.17.7)
Suggests hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit
Depends On Me
Imports Me VanillaICE
Suggests Me ArrayTV, hapmap370k, oligoClasses, SNPchip
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