subset_ontology_search: Perform ontology searches on up/down subsets of differential...

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

Perform ontology searches on up/down subsets of differential expression data.

Description

In the same way all_pairwise() attempts to simplify using multiple DE tools, this function seeks to make it easier to extract subsets of differentially expressed data and pass them to goseq, clusterProfiler, topGO, GOstats, and gProfiler.

Usage

subset_ontology_search(
  changed_counts,
  doplot = TRUE,
  do_goseq = TRUE,
  do_cluster = TRUE,
  do_topgo = TRUE,
  do_gostats = TRUE,
  do_gprofiler = TRUE,
  according_to = "limma",
  ...
)

Arguments

changed_counts	List of changed counts as ups and downs.
doplot	Include plots in the results?
do_goseq	Perform goseq search?
do_cluster	Perform clusterprofiler search?
do_topgo	Perform topgo search?
do_gostats	Perform gostats search?
do_gprofiler	Do a gprofiler search?
according_to	If results from multiple DE tools were passed, which one defines 'significant'?
...	Extra arguments!

Value

List of ontology search results, up and down for each contrast.

See Also

[goseq] [clusterProfiler] [topGO] [goStats] [gProfiler]

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