get_kegg_genes: Extract the set of geneIDs matching pathways for a given...

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

Extract the set of geneIDs matching pathways for a given species.

Description

This uses KEGGREST to extract the mappings for all genes for a species and pathway or 'all'. Because downloading them takes a while, it will save the results to kegg_species.rda. When run interactively, it will give some information regarding the number of genes observed in each pathway.

Usage

get_kegg_genes(
  pathway = "all",
  abbreviation = NULL,
  species = "leishmania major",
  savefile = NULL
)

Arguments

pathway	Either a single pathway kegg id or 'all'.
abbreviation	Optional 3 letter species kegg id.
species	Stringified species name used to extract the 3 letter abbreviation.
savefile	Filename to which to save the relevant data.

Value

Dataframe of the various kegg data for each pathway, 1 row/gene.

See Also

[KEGGREST]

Examples

## Not run: 
 kegg_info <- get_kegg_genes(species = "Canis familiaris")

## End(Not run)

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