RLMM

DOI: 10.18129/B9.bioc.RLMM  

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Bioconductor version: Release (3.16)

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 (version "4.2") and enter:

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

BiocManager::install("RLMM")

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("RLMM")

 

PDF	R Script	RLMM Doc
PDF		Reference Manual

Details

biocViews	GeneticVariability, Microarray, OneChannel, SNP, Software
Version	1.60.0
In Bioconductor since	BioC 1.8 (R-2.3) (17 years)
License	LGPL (>= 2)
Depends	R (>= 2.1.0)
Imports	graphics, grDevices, MASS, stats, utils
LinkingTo
Suggests
SystemRequirements	Internal files Xba.CQV, Xba.regions (or other regions file)
Enhances
URL	http://www.stat.berkeley.edu/users/nrabbee/RLMM
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	RLMM_1.60.0.tar.gz
Windows Binary	RLMM_1.60.0.zip
macOS Binary (x86_64)	RLMM_1.60.0.tgz
macOS Binary (arm64)	RLMM_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RLMM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RLMM
Bioc Package Browser	https://code.bioconductor.org/browse/RLMM/
Package Short Url	https://bioconductor.org/packages/RLMM/
Package Downloads Report	Download Stats