GSEA_ESpermutations: Calculate enrichment scores for a permutation test.

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

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)

LauraPS1/TFEA.ChIP documentation built on April 21, 2023, 7:29 a.m.