pmGSEA: poor mans GSEA

pmGSEAR Documentation

poor mans GSEA

Description

pmGSEA "poor man's GSEA " ***

Given a gene.set (character vector) or gene.sets (list of character vectors) and given a named vector of significance values or table of significant genes (sig.table) (if table then significance column is $p or first column) identifies gene sets that have significant negative deviation of a "signed K-S" statistic vs uniform distribution (ie have p values significantly clustering towards zero) ie are significantly enriched in genes showing positive selection.

if positive.selection = F, will identify sets with significantly positive deviation of a "signed K-S" statistic (ie have p values significantly clustering towards 1) these are sets showig significant negative selection.

All p-values are computed against a distribution of signed K-S statistic obtained through permutation using random gene sets of the same size chosen from sig.table

Will adaptively perform permutations between minperms and maxperms using following rule of thumb: if there are <PERM.THRESH permutations with greater than (lower.tail = F) or less than (lower.tail = T) score than observed score, then will compute additional perms

*** actually not much poorer than the original GSEA, basically a reimplementation of Mootha et al Nat Gen 2002

Usage

pmGSEA(
  gene.sets,
  sig.table,
  min.perms = 100,
  max.perms = 1e+05,
  positive.selection = T,
  length.filter = F,
  length.range = c(5, 50),
  mc.cores = 1,
  plot.hist = F,
  verbose = F,
  bootstrap = T,
  rank.test = F
)

Arguments

gene.sets

a named list of character vectors, each list item is a gene set, i.e. a character vector of genes

sig.table

named vector of p values from an analysis e.g. mutSig, the names of the genes are

min.perms

minimum number of permutations to do in the adaptive permutation test

max.perms

maximum number of permutations to do in the adaptive permutation test

length.range

length 2 integer vector specifying min and max gene set size to score after intersection with genes in sig.table default: c(5,50)

Author(s)

Marcin Imielinski


mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.