load_kegg_annotations: Create a data frame of pathways to gene IDs from KEGGREST

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

Create a data frame of pathways to gene IDs from KEGGREST

Description

This seeks to take the peculiar format from KEGGREST for pathway<->genes and make it easier to deal with. Sadly, this only works for a subset of species now.

Usage

load_kegg_annotations(species = "coli", abbreviation = NULL, flatten = TRUE)

Arguments

species	String to use to query KEGG abbreviation.
abbreviation	If you already know the abbreviation, use it.
flatten	Flatten nested tables?

Value

dataframe with rows of KEGG gene IDs and columns of NCBI gene IDs and KEGG paths.

See Also

[KEGGREST]

Examples

 sc_kegg_annot <- load_kegg_annotations(species = "cerevisiae")
 head(sc_kegg_annot)

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