multi_fisher_enrichment: Fisher Exact Test of gene set enrichment with multiple...

In jdreyf/ezlimma: Streamlines and extends limma package

Fisher Exact Test of gene set enrichment with multiple vectors of significant genes with output to Excel

Description

Test enrichment of multiple vectors of significant genes against the universe of genes in feat.tab per gene set using fisher.test. It returns a data frame with statistics per gene set, and can write this to Excel. The Excel file links to CSV files, which contain statistics per genes in a set. If you only have one vector of significant genes, use fisher_enrichment.

Usage

multi_fisher_enrichment(
  sig.sets,
  G,
  feat.tab,
  name = NA,
  adjust.method = "BH",
  min.nfeats = 3,
  max.nfeats = 1000,
  pwy.nchar = 199
)

Arguments

sig.sets	Named list whose elements are vectors of significant gene IDs matching rownames(feat.tab).
G	Gene set list as returned from read_gmt.
feat.tab	Table of feature (e.g. gene) statistics that the Excel table can link to.
name	Name for the folder and Excel file that get written. Set to NA to avoid writing output.
adjust.method	Method used to adjust the p-values for multiple testing. Only for mroast.
min.nfeats	Minimum number of features (e.g. genes) needed in a gene set for testing.
max.nfeats	Maximum number of features (e.g. genes) needed in a gene set for testing.
pwy.nchar	Numeric maximum number of characters allowed in pathway name.

Details

Pathway (i.e. gene set) names are altered to be valid filenames in Windows and Linux. Numeric columns are rounded to 8 significant figures.

Value

List with two elements: pwy.stats, a table of pathway statistics; and feat.tab, a table that appends a binary matrix of which genes are in which sig.set and the input feat.tab.

See Also

fisher_enrichment

jdreyf/ezlimma documentation built on April 28, 2024, 1:10 p.m.