allSugarScoresForOneGenome: Calculate Completeness Of All Sugar Degradation Pathways...

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

Calculate Completeness Of All Sugar Degradation Pathways Within One Genome

Description

Use the calculateStepsForOneSugar function for all sugar pathways one by one, and build a named vector for all pathways.

Usage

allSugarScoresForOneGenome(geneVec, allSugars, ER)

Arguments

geneVec	A vector of gene names, representing all sugar degradation enzymes present in one genome of interest.
allSugars	A vector of all sugar degradation pathways.
ER	A data.frame describing enzymatic reactions with at least 3 columns: "Gene" for gene encoding an enzyme, "Reaction.EC" for categorization of catalytic reactions, and "Sugar" for degradation pathway. Column names need to be EXACTLY the same, case sensitive.

Value

A vector containing a genome's score for all sugar degradation pathways.

Examples

## Not run: 
 geneVec <- c("rpe", "rpiB", "eno", "fucK")
 ER <- microCompet::EnzymaticReactions
 ED <- microCompet::EnzymeDistribution
 allSugars <- sort(unique(ED$Sugar))
 sugarScoreVec <- allSugarScoresForOneGenome(geneVec, allSugars, ER)
 sugarScoreVec

## End(Not run)

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