RLMM
This is the development version of RLMM; for the stable release version, see RLMM.
A Genotype Calling Algorithm for Affymetrix SNP Arrays
Bioconductor version: Development (3.24)
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("RLMM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| RLMM Doc | R Script | |
| Reference Manual |
Details
| biocViews | GeneticVariability, Microarray, OneChannel, SNP, Software |
| Version | 1.75.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (20.5 years) |
| License | LGPL (>= 2) |
| Depends | R (>= 2.1.0) |
| Imports | graphics, grDevices, MASS, stats, utils |
| System Requirements | Internal files Xba.CQV, Xba.regions (or other regions file) |
| URL | http://www.stat.berkeley.edu/users/nrabbee/RLMM |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RLMM_1.75.0.tar.gz |
| Windows Binary (x86_64) | RLMM_1.75.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | RLMM_1.75.0.tgz |
| macOS Binary (sonoma-arm64) | RLMM_1.75.0.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 |