gene2rxn: gene to reaction lookup

In maxconway/metabex: Metabolic Model Explorer

Description

Takes a sybil model and a data frame or vector of gene activity, and finds active reactions from this.

Usage

gene2rxn(genes, model, env = new.env(emptyenv()))

## S3 method for class 'data.frame'
gene2rxn(genes, model, env = new.env(emptyenv()))

## S3 method for class 'numeric'
gene2rxn(genes, model, env = new.env(emptyenv()),
  exprlist = NULL)

Arguments

genes	a data frame or vector of gene activity. If a data frame, columns should be genes.
model	a sybil model.
env	an environment in which to evaluate the gene-reaction mappings.
exprlist	model@gprRules, parsed to expressions. Mainly for internal use.

Details

Works by creating a new environment and evaluating gpr rules computationally. Could be a security concern, so check what you're choosing to run. Is also quite slow, if general.

Value

a vector of reaction presence or activity

maxconway/metabex documentation built on May 21, 2019, 1:39 p.m.