pmGSEA | R Documentation |
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
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
)
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) |
Marcin Imielinski
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.