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 3.2 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: 3.2

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 at unicamp.br>, 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:

## try http:// if https:// URLs are not supported
source("https://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 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

Details

biocViews CopyNumberVariation, Microarray, Preprocessing, SNP, Software
Version 1.28.2
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, oligoClasses, SNPchip
Build Report

Package Archives

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

Package Source crlmm_1.28.2.tar.gz
Windows Binary crlmm_1.28.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) crlmm_1.28.0.tgz
Mac OS X 10.9 (Mavericks) crlmm_1.28.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/crlmm/tree/release-3.2
Package Short Url http://bioconductor.org/packages/crlmm/
Package Downloads Report Download Stats

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