GSEA_gene_multiple: Do GSEA for a list of geneSets based on random permuted or...

In jmzeng1314/geneSet:

Description

It'll do GSEA Tests for a list of geneSets according to the signal 2 noise values for all of the genes or other values,such as foldchange. It'll return ES ,the running ES score for all of the genes, a numeric vector . rand_es ,the maximal running ES score for each permutation, a numeric vector. p which calculated by formule:p <- 1-pnorm((max(ES)-mean(rand_es))/sd(rand_es))

Usage

GSEA_gene_multiple(gene_values = rnorm(100), gene_names = 1:100,
  geneSet_list = list(set1 = sample(1:100, 10), set2 = sample(1:100, 10)),
  n = 1000)

Arguments

gene_values	A vector of values for each gene,most of time it's signal 2 noise.
gene_names	A vector of names for each gene
geneSet_list	A list which contains all of the vector for each geneSet.
n	Times for random permuted or bootstraps by genes,default:1000

Value

a list contain 4 elements: ES,rand_es, p and ismem

Examples

GSEA_gene_multiple()

jmzeng1314/geneSet documentation built on May 19, 2019, 2:57 p.m.