getpaths_frmEnds: Get (KEGG) biological pathways from end point

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

Get (KEGG) biological pathways from end point

Description

getpaths_frmEnds returns a list of (KEGG) pathways from an input gene end-point.

Usage

getpaths_frmEnds(gene_entrez, hsapien_mart, kgmlDir = getwd(), saveKGML = TRUE)

Arguments

gene	character or numeric (Entrez ID)

Details

This function requires the input of a single gene (in Entrez ID format) from this it will search the KEGG database for any pathways which include the gene. This is done by converting the Entrez ID into a KEGG human gene ID (E.g. 1234 becomes hsa:1234). The pathways in which the gene is present are then filtered to only include those where the gene is an "end-point" for the pathway: I.e. it has one or more inward-facing edges and no outward-facing edges. These pathways are those which are passed to return() If no pathways are found or the gene is present in pathways but is not an end-point, the function will inform the user and will return nothing.

Examples

## Search for pathways in KEGG which have IL18 as an end-point.
getpaths_frmEnds(3606)

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