transcript_check: Check whether a gene is transcribed via the pathway (I.e. via...

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

Check whether a gene is transcribed via the pathway (I.e. via interaction with DNA)

Description

transcript_check returns a single row of a data frame, containing the interactions leading to it in KEGG.

Usage

transcript_check(pathway, gene_entrez, kegg_file = "./")

Arguments

pathway	character. KEGG pathway ID (e.g.: hsa05131).
gene_entrez	character or numeric. Entrez gene ID.
kegg_file	character. Full file location of a KEGG KGML file.

Details

This function uses a defined KEGG KGML, pathway name, and Entrz gene. It searches the KGML for this gene (only in nodes which the gene is at the end of an interaction) and then returns those rows to the function user. If the "type" of interaction is GErel, this is defined by KEGG as "gene expression interaction, indicating relation of transcription factor and target gene product" and therefore, this is a gene product which is transcribed through the pathway.

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