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

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

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.

Usage

load_kegg_annotations(
  gene_table,
  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.

Author(s)

atb

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.