goseq2enrich: Create a clusterProfiler compatible enrichResult data...

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

Create a clusterProfiler compatible enrichResult data structure from a goseq result.

Description

The metrics and visualization methods in clusterProfiler are the best. It is not always trivial to get non-model organisms working well with clusterProfiler. Therefore I still like using tools like topgo/goseq/gostats/gprofiler. This function and its companions seek to make them cross-compatible. Ideally, they will lead me to being able to rip out a lot of superfluous material.

Usage

goseq2enrich(
  retlist,
  ontology = "MF",
  cutoff = 1,
  cutoff_column = "over_represented_pvalue",
  organism = NULL,
  padjust_method = "BH"
)

Arguments

retlist	Result from simple_goseq().
ontology	Ontology sub-tree of interest.
cutoff	(adjusted)p cutoff.
cutoff_column	Choose a column of p-values.
organism	Currently unused.
padjust_method	Define the desired p.adjust method.

Value

enrichResult object ready to pass to things like dotplot.

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