To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("crlmm")

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

crlmm

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see crlmm.

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

Bioconductor version: 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")):

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("crlmm")

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

biocViews	CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version	1.24.0
In Bioconductor since	BioC 2.4 (R-2.9) (7 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 (>= 0.3.1.2.1), matrixStats, VGAM, parallel
LinkingTo	preprocessCore(>= 1.17.7)
Suggests	hapmapsnp6, genomewidesnp6Crlmm(>= 1.0.7), GGdata, snpStats, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	VanillaICE
Suggests Me	ArrayTV, hapmap370k, SNPchip
Build Report

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
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/crlmm/tree/release-3.0
Package Short Url	http://bioconductor.org/packages/crlmm/
Package Downloads Report	Download Stats