kegg_geneglob: Obtain all genes from a KEGG pathway

In Sabor117/PathWAS: Creates predictive models of biological pathway functionality

Obtain all genes from a KEGG pathway

Description

Returns all genes associated with input pathway (excluding directionality)

Usage

kegg_geneglob(pathway, in_mart = NULL)

Arguments

pathway	character. KEGG pathway ID.
in_mart	data frame. A data frame of multiple columns which, at a minimum includes entrezgene_id and external_gene_name.

Details

This function takes a pathway (possibly defined by the getpaths_frmEnds function) from KEGG and then finds all genes associated with this pathway and outputs that. Depending on whether or not you have an available BioMart reference table, this can be either as a list of Entrez IDs or as a data frame of KEGG IDs (which is simply "hsa:ENTREZ-ID") and gene names. A BioMart table can be obtained either by downloading a full dataset from https://www.ensembl.org/biomart/martview/ or through usage of the biomaRt package. This table MUST have the entrezgene_id and external_gene_name columns (default column names in BioMart for Entrez and gene names).

Sabor117/PathWAS documentation built on Nov. 29, 2024, 7:44 a.m.