runGSEA: Gene Set Enrichement Analysi on GF-ICF

In dibbelab/gficf: Gene Frequency - Inverse Cell Frequency

Gene Set Enrichement Analysi on GF-ICF

Description

Compute GSEA for each cluster across a set of input pathways.

Usage

runGSEA(
  data,
  gmt.file,
  nsim = 1000,
  convertToEns = T,
  convertHu2Mm = F,
  nt = 2,
  minSize = 15,
  maxSize = Inf,
  verbose = TRUE,
  seed = 180582,
  method = "GSEA"
)

Arguments

data	list; GFICF object
gmt.file	characters; Path to gmt file from MSigDB
nsim	integer; number of simulation used to compute ES significance.
convertToEns	boolean: Convert gene sets from gene symbols to Ensable id.
convertHu2Mm	boolean: Convert gene sets from human symbols to Mouse Ensable id.
nt	numeric; Number of cpu to use for the GSEA
minSize	numeric; Minimal size of a gene set to test (default 15). All pathways below the threshold are excluded.
maxSize	numeric; Maximal size of a gene set to test (default Inf). All pathways above the threshold are excluded.
verbose	boolean; Show the progress bar.
seed	integer; Seed to use for random number generation.
method	string; Method to use GSEA or GSVA. Default is GSEA.

Value

The updated gficf object.

dibbelab/gficf documentation built on Nov. 2, 2022, 2:28 a.m.