GSEA_EnrichmentScore: Computes the weighted GSEA score of gene.set in gene.list.

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Computes the weighted GSEA score of gene.set in gene.list.

Description

Computes the weighted GSEA score of gene.set in gene.list.

Usage

GSEA_EnrichmentScore(
  gene.list,
  gene.set,
  weighted.score.type = 0,
  correl.vector = NULL
)

Arguments

gene.list	The ordered gene list
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

Value

list of: ES: Enrichment score (real number between -1 and +1) arg.ES: Location in gene.list where the peak running enrichment occurs (peak of the 'mountain') RES: Numerical vector containing the running enrichment score for all locations in the gene list tag.indicator: Binary vector indicating the location of the gene sets (1's) in the gene list

Examples

GSEA_EnrichmentScore(gene.list=c('3091','2034','405','55818'),
gene.set=c('2034','112399','405'))

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