runGost: a wrapper for 'gprofiler2"s 'gost' function

In raim/segmenTools: Tools for Functional Genome Exploration

a wrapper for gprofiler2's gost function

Description

takes a gene clustering, a named vector of gene categories, where the names are gene IDs, and calls the gost function of the gprofiler2 to do enrichment analysis for all gene annotations available. It then parses the output of the gost function of the gprofiler2 R package into overlap tables for use with segmenTools' cluster analysis pipeline.

Usage

runGost(
  cls,
  organism = "hsapiens",
  cls.srt,
  categories,
  terms,
  verb = 1,
  significant = FALSE,
  ...
)

Arguments

cls	a name vector of a gene classification, where the names are gene IDs recognized by gprofiler2 in the respective organism,
organism	the organism ID to which gene IDs of the cls argument refer to; see ?gprofiler2::gost,
cls.srt	an optional sorting of gene classes in cls,
categories	annotation source categories to report,
terms	list of annotation terms to report (over all categories), a name list of terms to report,
verb	level of verbosity, 0: no output, 1: progress messages,
significant	only report significant hits, option to gost.
...	further arguments to gprofiler2's gost function.

raim/segmenTools documentation built on May 5, 2024, 11:30 a.m.