To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("RLMM")
In most cases, you don't need to download the package archive at all.
RLMM
A Genotype Calling Algorithm for Affymetrix SNP Arrays
Bioconductor version: 3.1
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>
Citation (from within R,
enter citation("RLMM")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://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")
| R Script | RLMM Doc | |
| Reference Manual |
Details
| biocViews | GeneticVariability, Microarray, OneChannel, SNP, Software |
| Version | 1.30.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (9.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RLMM_1.30.0.tar.gz |
| Windows Binary | RLMM_1.30.0.zip |
| Mac OS X 10.6 (Snow Leopard) | RLMM_1.30.0.tgz |
| Mac OS X 10.9 (Mavericks) | RLMM_1.30.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/RLMM/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/RLMM/ |
| Package Downloads Report | Download Stats |
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