crlmm

DOI: 10.18129/B9.bioc.crlmm    

This package is for version 3.9 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: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crlmm")

For older versions of R, please refer to the appropriate Bioconductor release.

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	R Script	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	1.42.0
In Bioconductor since	BioC 2.4 (R-2.9) (10.5 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 (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot
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
Links To Me
Build Report

Package Archives

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

Source Package	crlmm_1.42.0.tar.gz
Windows Binary	crlmm_1.42.0.zip
Mac OS X 10.11 (El Capitan)	crlmm_1.42.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/crlmm
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/crlmm
Package Short Url	https://bioconductor.org/packages/crlmm/
Package Downloads Report	Download Stats