SMPDB2G: Transform SMPDB protein and/or metabolite pathway data frames...

In jdreyf/ezlimma: Streamlines and extends limma package

Transform SMPDB protein and/or metabolite pathway data frames into a pathway object

Description

Transform SMPDB protein and/or metabolite pathway data frames, read in as CSV files from http://smpdb.ca/downloads, into a pathway object that matches Pathway Commons, using Gene.Name to identify proteins and ChEBI IDs for metabolites. Format of SMPDB downloads has changed, so now it has numerous semi-redundant fatty acid pathways, so this will need to be modified if want to stay up to date with SMPDB.

Usage

SMPDB2G(smpdb.prot, smpdb.met, exclude.pwy.subj = NA)

Arguments

smpdb.prot	Data frame of proteins per pathway from SMPDB.
smpdb.met	Data frame of metabolites per pathway from SMPDB.
exclude.pwy.subj	Vector of subjects (or types) of pathways to exclude

jdreyf/ezlimma documentation built on June 11, 2025, 3:53 p.m.