RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Bioconductor version: 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 <nrabbee at post.harvard.edu>, Gary Wong <wongg62 at berkeley.edu>

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("RLMM")

Documentation

PDF R Script RLMM Doc
PDF   Reference Manual

Details

biocViews Microarray, OneChannel, SNP, GeneticVariability
Depends R (>= 2.1.0)
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 1.14.0
Since Bioconductor 1.8 (R-2.3)

Package Downloads

Package Source RLMM_1.14.0.tar.gz
Windows Binary RLMM_1.14.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary RLMM_1.14.0.tgz
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