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.