README.md

In billyhw/GSALightning: Fast Permutation-based Gene Set Analysis

Motivation

GSA-Lightning is an R package that provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.

Installation

GSA-Lightning requires R 3.3.0 or above (https://www.r-project.org/).

We recommend using the R "devtools" package to install GSALightning from Github.

To install devtools, in an R prompt type:

install.packages("devtools")

To use devtools to install GSA-Lightning, type:

devtools::install_github("billyhw/GSALightning")

Since the package contains some large example gene expression data sets, the download time may take 1-3 minutes. Please kindly be patient.

If the R vignette is also desired, use instead:

library(devtools)
install_github("billyhw/GSALightning", build_vignette = TRUE)

Note the vignette will take some time to build (4-5 minutes) due to some large-scale analysis examples included in the vignette.

The Bioconductor stable release of GSA-Lightning is at:

https://bioconductor.org/packages/release/bioc/html/GSALightning.html

Code

Please consult the R help page of GSA-Lightning for examples:

? GSALight

Contributor

Billy Heung Wing Chang ([e-mail])

Reference

Billy Heung Wing Chang and Weidong Tian (2016) GSA-Lightning: Ultra-fast Permutation-based Gene Set Analysis. Bioinformatics. doi: 10.1093/bioinformatics/btw349

http://bioinformatics.oxfordjournals.org/content/early/2016/06/11/bioinformatics.btw349.abstract

License

GPL (>=2)

billyhw/GSALightning documentation built on May 12, 2019, 9:22 p.m.