randRotation
This is the released version of randRotation; for the devel version, see randRotation.
Random Rotation Methods for High Dimensional Data with Batch Structure
Bioconductor version: Release (3.23)
A collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods.
Author: Peter Hettegger [aut, cre]
Maintainer: Peter Hettegger <p.hettegger at gmail.com>
citation("randRotation")):
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")
BiocManager::install("randRotation")
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("randRotation")| Random Rotation Package Introduction | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, BiomedicalInformatics, DifferentialExpression, GeneExpression, Genetics, MicroRNAArray, Microarray, Normalization, Preprocessing, RNASeq, Sequencing, Software, StatisticalMethod |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-3 |
| Depends | |
| Imports | methods, graphics, utils, stats, Rdpack (>= 0.7) |
| System Requirements | |
| URL | https://github.com/phettegger/randRotation |
| Bug Reports | https://github.com/phettegger/randRotation/issues |
See More
| Suggests | knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva |
| 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 | randRotation_1.23.0.tar.gz |
| Windows Binary (x86_64) | randRotation_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | randRotation_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/randRotation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/randRotation |
| Bioc Package Browser | https://code.bioconductor.org/browse/randRotation/ |
| Package Short Url | https://bioconductor.org/packages/randRotation/ |
| Package Downloads Report | Download Stats |