GSEA_run: Function to run a GSEA analysis

In TFEA.ChIP: Analyze Transcription Factor Enrichment

Description

Function to run a GSEA to analyze the distribution of TFBS across a sorted list of genes.

Usage

GSEA_run(gene.list, LFC, chip_index = get_chip_index(),
  get.RES = FALSE, RES.filter = NULL, perms = 1000)

Arguments

gene.list	List of Entrez IDs ordered by their fold change.
LFC	Vector of log2( Fold Change ) values.
chip_index	Output of the function <e2><80><9c>get_chip_index<e2><80><9d>, a data frame containing accession IDs of ChIPs on the database and the TF each one tests. If not provided, the whole internal database will be used
get.RES	(Optional) boolean. If TRUE, the function stores Running Enrichment Scores of all/some TF.
RES.filter	(Optional) chr vector. When get.RES==TRUE, allows to choose which TF's Running Enrichment Score to store.
perms	Number of permutations for a permutation test.

Value

a list of: Enrichment.table: data frame containing accession ID, Cell type, ChIP-Seq treatment, transcription factor tested, enrichment score, raw and adjusted p-value, and argument of every ChIP-Seq experiment. RES (optional): list of running sums of every ChIP-Seq indicators (optional): list of 0/1 vectors that stores the matches (1) and mismatches (0) between the gene list and the gene set.

Examples

data('hypoxia',package = 'TFEA.ChIP')
preprocessInputData(hypoxia)
chip_index<-get_chip_index(TFfilter = c('HIF1A','EPAS1','ARNT'))
GSEA.result <- GSEA_run( hypoxia$Genes, hypoxia$log2FoldChange, chip_index, get.RES = TRUE)

TFEA.ChIP documentation built on Nov. 8, 2020, 5:05 p.m.