getCustomPathwayFromAnalyte: Utility method supporting pathway analyses when file-based...

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

Utility method supporting pathway analyses when file-based pathway lists are used rather than the ramp database.

Description

Utility method supporting pathway analyses when file-based pathway lists are used rather than the ramp database.

Usage

getCustomPathwayFromAnalyte(analytes, pathways, analyte_type)

Arguments

analytes	a vector of analytes (genes or metabolites) that need to be searched
pathways	If "RaMP" (default), use pathway definitions within RaMP-DB. Else, supply path to gmx file containing custom pathway definitions. GMX files are a tab-separated format that contain one analyte set per column, with the name of the set in the first row, and constituent analytes in subsequent rows
analyte_type	"genes" or "metabolites"

Value

A pathwaydf compatible with runFisherTest

Author(s)

Andrew Patt

ncats/RaMP-DB documentation built on June 1, 2024, 9:34 p.m.