GSEA_ESpermutations {TFEA.ChIP}R Documentation

Calculate enrichment scores for a permutation test.

Description

Function to calculate enrichment scores over a randomly ordered gene list.

Usage

GSEA_ESpermutations(gene.list, gene.set, weighted.score.type = 0,
  correl.vector = NULL, perms = 1000)

Arguments

gene.list

Vector of gene Entrez IDs.

gene.set

A gene set, e.g. gene IDs corresponding to a ChIP-Seq experiment's peaks.

weighted.score.type

Type of score: weight: 0 (unweighted = Kolmogorov-Smirnov), 1 (weighted), and 2 (over-weighted)

correl.vector

A vector with the coorelations (such as signal to noise scores) corresponding to the genes in the gene list

perms

Number of permutations

Value

Vector of Enrichment Scores for a permutation test. gene.set=c('2034','112399','405'), perms=10)


[Package TFEA.ChIP version 1.4.2 Index]