pct_all_kegg: Extract the percent differentially expressed genes for all...

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

Extract the percent differentially expressed genes for all KEGG pathways.

Description

KEGGgraph provides some interesting functionality for mapping KEGGids and examining the pieces. This attempts to use that in order to evaluate how many 'significant' genes are in a given pathway.

Usage

pct_all_kegg(
  all_ids,
  sig_ids,
  organism = "dme",
  pathways = "all",
  pathdir = "kegg_pathways",
  verbose = FALSE,
  ...
)

Arguments

all_ids	Set of all gene IDs in a given analysis.
sig_ids	Set of significant gene IDs.
organism	KEGG organism identifier.
pathways	What pathways to look at?
pathdir	Directory into which to copy downloaded pathway files.
verbose	Talky talky?
...	Options I might pass from other functions are dropped into arglist.

Value

Dataframe including the filenames, percentages, nodes included, and differential nodes.

See Also

[KEGGgraph] [KEGGREST]

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