gprofiler2enrich: Recast gProfiler data to the output class produced by...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Recast gProfiler data to the output class produced by clusterProfiler.

Description

I would like to use the various clusterProfiler plots more easily. Therefore I figured it would be advantageous to coerce the various outputs from gprofiler and friends into the datastructure produced by clusterProfiler.

I would like to use the various clusterProfiler plots more easily. Therefore I figured it would be advantageous to coerce the various outputs from gprofiler and friends into the datastructure produced by clusterProfiler.

Usage

gprofiler2enrich(
  retlst,
  ontology = "MF",
  cutoff = 1,
  organism = NULL,
  padjust_method = "BH"
)

gprofiler2enrich(
  retlst,
  ontology = "MF",
  cutoff = 1,
  organism = NULL,
  padjust_method = "BH"
)

Arguments

retlst	Output from simple_gprofiler()
ontology	Category type to extract, currently only GO?
cutoff	Use a p-value cutoff to get only the significant categories?
organism	Set the orgdb organism name?
padjust_method	what it says on the tin.
retlist	Output from simple_gprofiler()

Value

enrichResult object ready to pass to things like dotplot.

The same 'enrich' datastructure produced by clusterProfiler.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.