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

RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Bioconductor version: 2.13

A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

Author: Nusrat Rabbee <nrabbee at post.harvard.edu>, Gary Wong <wongg62 at berkeley.edu>

Maintainer: Nusrat Rabbee <nrabbee at post.harvard.edu>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("RLMM")

 

PDF	R Script	RLMM Doc
PDF		Reference Manual

Details

biocViews	GeneticVariability, Microarray, OneChannel, SNP, Software
Version	1.24.0
In Bioconductor since	BioC 1.8 (R-2.3)
License	LGPL (>= 2)
Depends	R (>= 2.1.0)
Imports	graphics, grDevices, MASS, stats, utils
Suggests
System Requirements	Internal files Xba.CQV, Xba.regions (or other regions file)
URL	http://www.stat.berkeley.edu/users/nrabbee/RLMM
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source	RLMM_1.24.0.tar.gz
Windows Binary	RLMM_1.24.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	RLMM_1.24.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats