createEdgeFrame: Create A Data.frame To Represent All Edges in fullNetwork

In MolyWang/microCompet: Identify A Microbe's Potential Nutrition Competitor From Microbiota

Create A Data.frame To Represent All Edges in fullNetwork

Description

Given a list of enzymatic reactions, extract unique reactions, count number of genes encoding enzymes that catalyze each reaction. This is a helper function defined for constructFullNetwork and is called only internally.

Usage

createEdgeFrame(relevantReactions)

Arguments

relevantReactions

A data.frame of enzymatic reactions, containing the required columns: Gene, Substrate, Product, Sugar (case sensitive).

Value

A data.frame with 4 columns. Substrate and Product are tail and head of each edge; NumOfEnzymes is count of enzymes that can catalyze the reaction; Sugar is the simple sugar degradation pathway this reaction is one step of.

Examples

## Not run: 
 library("microCompet")
 ER <- microCompet::EnzymaticReactions
 relevantReactions <- ER[ER$Sugar == "ribose", ]
 edgeFrame <- createEdgeFrame(relevantReactions)
 edgeFrame

## End(Not run)

MolyWang/microCompet documentation built on Feb. 26, 2023, 9:29 p.m.