getCustomPathwayFromAnalyte: Reads an excel file containing metabolite and gene...

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

Reads an excel file containing metabolite and gene annotations and filters pathways to those pathways represented by the input analytes.

Description

Reads an excel file containing metabolite and gene annotations and filters pathways to those pathways represented by the input analytes.

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 Oct. 28, 2023, 8:12 a.m.