pct_kegg_diff: Extract the percent differentially expressed genes in a given...

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

Extract the percent differentially expressed genes in a given KEGG pathway.

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_kegg_diff(
  all_ids,
  sig_ids,
  pathway = "00500",
  organism = "dme",
  pathdir = "kegg_pathways",
  ...
)

Arguments

all_ids	Set of all gene IDs in a given analysis.
sig_ids	Set of significant gene IDs.
pathway	Numeric pathway identifier.
organism	KEGG organism identifier.
pathdir	Directory into which to copy downloaded pathway files.
...	Options I might pass from other functions are dropped into arglist.

Value

Percent genes/pathway deemed significant.

See Also

[KEGGgraph] [KEGGREST]

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