RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

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

Vignettes (Documentation)

Package Downloads

RLMM.pdf
Source RLMM_1.2.0.tar.gz
Windows binary RLMM_1.2.0.zip
OS X binary RLMM_1.2.0.tgz

Details

biocViews
Depends R, MASS
Suggests
Imports
SystemRequirements Internal files Xba.CQV, Xba.regions (or other regions file)
License LGPL version 2 or newer
URL http://www.stat.berkeley.edu/users/nrabbee/RLMM
dependsOnMe
suggestsMe