To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")

In most cases, you don't need to download the package archive at all.

crlmm

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

Bioconductor version: Release (3.0)

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

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

Maintainer: Benilton S Carvalho <Benilton.Carvalho at cancer.org.uk>, Robert Scharpf <rscharpf at jhsph.edu>, Matt Ritchie <mritchie at wehi.EDU.AU>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("crlmm")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("crlmm")

 

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

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version 1.24.0
In Bioconductor since BioC 2.4 (R-2.9)
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 (>= 0.3.1.2.1), matrixStats, VGAM, parallel
Suggests hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit
System Requirements
URL
Depends On Me
Imports Me
Suggests Me ArrayTV, hapmap370k, SNPchip, VanillaICE

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source crlmm_1.24.0.tar.gz
Windows Binary crlmm_1.24.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) crlmm_1.24.0.tgz
Mac OS X 10.9 (Mavericks) crlmm_1.24.0.tgz
Browse/checkout source (username/password: readonly)
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