gsea: Enrichment analysis for any type of annotation data

In guokai8/EnrichR: Functional Enrichment analysis

Description

Enrichment analysis for any type of annotation data

Usage

gsea(
  x,
  annot,
  annot.info = NULL,
  minSize = 15,
  maxSize = 500,
  nperm = 5000,
  filename = NULL,
  padj.method = "BH",
  table = TRUE
)

Arguments

x	a vector include all log2FC with gene name
annot	annotation file for all genes
annot.info	Term with annotation details
minSize	Minimal size of a gene set to test. All pathways below the threshold are excluded.
maxSize	Maximal size of a gene set to test. All pathways above the threshold are excluded.
nperm	Number of permutations to do. Minimial possible nominal p-value is about 1/nperm
filename	output filename
padj.method	p value adjust method

Author(s)

Kai Guo

guokai8/EnrichR documentation built on May 18, 2020, 5:29 a.m.