GSALightning-package {GSALightning} | R Documentation

## Fast Permutation-based Gene Set Analysis

### Description

GSALightning 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.

### Details

Index of help topics:

    GSALight                Fast Permutation-based Gene Set Analysis
    GSALightning-package    Fast Permutation-based Gene Set Analysis
    expression              Breast Cancer Data from The Cancer Genome Atlas
                            (TCGA)
    permTestLight           Fast Single-Gene Permutation Test
    sampleInfo              Sample Information for the Breast Cancer Data
                            from The Cancer Genome Atlas (TCGA)
    targetGenes             Target Genes of Distal Regulatory Elements
    wilcoxTest              Single-Gene Mann Whitney Wilcoxon Test

### Author(s)

Billy Heung Wing Chang

Maintainer: Billy Heung Wing Chang <billyheungwing@gmail.com>

### References

BHW Chang and W Tian (2015). GSA-Lightning: Ultra Fast Permutation-based Gene Set Analysis. Bioinformatics. doi: 10.1093/bioinformatics/btw349

B Efron and RJ Tibshirani (2007). "On testing the significance of sets of genes." The annals of applied statistics 1(1):107-129

### See Also

`GSALight`, `permTestLight`.

[Package GSALightning version 1.8.0 Index]