RegParallel

DOI: 10.18129/B9.bioc.RegParallel    

Standard regression functions in R enabled for parallel processing over large data-frames

Bioconductor version: Release (3.13)

In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'.

Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su [aut]

Maintainer: Kevin Blighe <kevin at clinicalbioinformatics.co.uk>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RegParallel")

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("RegParallel")

 

HTML	R Script	Standard regression functions in R enabled for parallel processing over large data-frames
PDF		Reference Manual
Text		NEWS

Details

biocViews	DiseaseModel, ExperimentData
Version	1.10.0
License	GPL-3
Depends	doParallel, foreach, parallel, iterators, data.table, stringr, survival, arm, stats, utils, methods
Imports
LinkingTo
Suggests	RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/kevinblighe/RegParallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RegParallel_1.10.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/RegParallel
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RegParallel
Package Short Url	https://bioconductor.org/packages/RegParallel/
Package Downloads Report	Download Stats