RLMM
A Genotype Calling Algorithm for Affymetrix SNP Arrays
Bioconductor version: 3.23 · Package version: 1.74.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RLMM")Details
| Maintainer | Nusrat Rabbee <nrabbee@post.harvard.edu> |
| Author | Nusrat Rabbee <nrabbee@post.harvard.edu>, Gary Wong <wongg62@berkeley.edu> |
| License | LGPL (>= 2) |
| URL | http://www.stat.berkeley.edu/users/nrabbee/RLMM |
| System Requirements | Internal files Xba.CQV, Xba.regions (or other regions file) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneticVariability, Microarray, OneChannel, SNP, Software |
| Package Short Url | https://bioconductor.org/packages/RLMM/ |
Citation
From within R, enter citation("RLMM"):
Nusrat Rabbee, Gary Wong. RLMM: A Genotype Calling Algorithm for Affymetrix SNP Arrays. doi:10.18129/B9.bioc.RLMM, R package version 1.74.0, https://bioconductor.org/packages/RLMM.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RLMM_1.74.0.tar.gz |
| Windows binary (x86_64) | RLMM_1.74.0.zip |
| macOS binary (arm64) | RLMM_1.74.0.tgz |
| macOS binary (x86_64) | RLMM_1.74.0.tgz |