enrich_fgsea: Enrichment analysis for any type of annotation data

Description Usage Arguments Author(s)

View source: R/fgsea.R

Description

Enrichment analysis for any type of annotation data

Usage

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

Arguments

x:

a vector include all log2FC with gene name

annot:

annotation file for all genes

annot.info:

Term of all annotation

filenam:

output filename

padj.method:

p value adjust method

nperm:

Number of permutations to do. Minimial possible nominal p-value is about 1/nperm

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.

Author(s)

Kai Guo


hurlab/RichR documentation built on July 30, 2018, 10:13 p.m.