RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Bioconductor version: Development (2.8)

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, Gary Wong

Maintainer: Nusrat Rabbee

To install this package, start R and enter:

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

Documentation

PDF

R Script

RLMM Doc

Reference Manual

Details

biocViews	Microarray, OneChannel, SNP, GeneticVariability
Depends	R
Imports	graphics, grDevices, MASS, stats, utils
Suggests
System Requirements	Internal files Xba.CQV, Xba.regions (or other regions file)
License	LGPL (>= 2)
URL	http://www.stat.berkeley.edu/users/nrabbee/RLMM
Depends On Me
Imports Me
Suggests Me
Version	1.13.0

Package Downloads

Package Source	RLMM_1.13.0.tar.gz
Windows Binary	RLMM_1.13.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	RLMM_1.13.0.tgz
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