go_analysis: Run GOstats functional enrichment analysis for a list of...

In VallejosGroup/rvallejo: Shared analysis code and tools for the Vallejos Group

Description

Runs the conditional GOstats algorithm for a set of genes in a given universe. This function runs the algorithm for multiple ontologies, and returns a table of merged results.

Usage

go_analysis(
  genes,
  universe,
  annotation_package,
  ontologies = c("BP", "CC", "MF"),
  min_size = 3,
  mdlinks = TRUE,
  p_value = 0.01
)

Arguments

genes	The genes of interest; ie the balls drawn from the urn in the classical hypergeometric analogy. Should be ENTREZ IDs.
universe	The background set of genes. This corresponds to the bag of balls in the classical hypergeometric analogy. Should be ENTREZ IDs.
annotation_package	An organism annotation package used by the GOstats functions internally to annotate genes with GO terms and to traverse the GO hierarchy. eg, for humans, org.Hs.eg.db would be suitable and would require Entrez IDs for the genes and universe arguments.
ontologies	The ontologies to test. Options are "BP" (biological process), "CC" (cellular component) and "MF" (molecular function).
min_size	The minimum size of GO terms to include. It is advised to set this to at least 2; otherwise you will observe quite a few terms which are comprised of only a single gene.
mdlinks	Should the GO IDs be hyperlinked using Markdown in the output table?
p_value	p-value cutoff. This is important to set a priori, as it affects the conditional algorithm.

VallejosGroup/rvallejo documentation built on Jan. 29, 2021, 2:41 p.m.