ResidualMatrix
This is the development version of ResidualMatrix; for the stable release version, see ResidualMatrix.
Creating a DelayedMatrix of Regression Residuals
Bioconductor version: Development (3.24)
Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.
Author: Aaron Lun [aut, cre, cph]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("ResidualMatrix")):
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("ResidualMatrix")
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("ResidualMatrix")| Using the ResidualMatrix | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DataRepresentation, ExperimentalDesign, Regression, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | |
| Imports | methods, Matrix, S4Vectors, DelayedArray |
| System Requirements | |
| URL | https://github.com/LTLA/ResidualMatrix |
| Bug Reports | https://github.com/LTLA/ResidualMatrix/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, BiocSingular |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | batchelor |
| Suggests Me | alabaster.matrix, BiocSingular, chihaya, scran |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ResidualMatrix_1.23.0.tar.gz |
| Windows Binary (x86_64) | ResidualMatrix_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | ResidualMatrix_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | ResidualMatrix_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ResidualMatrix |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ResidualMatrix |
| Bioc Package Browser | https://code.bioconductor.org/browse/ResidualMatrix/ |
| Package Short Url | https://bioconductor.org/packages/ResidualMatrix/ |
| Package Downloads Report | Download Stats |