calculateStepsForOneSugar: Calculate Number Of Sugar Specific Degradation Enzymes In A...

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

Calculate Number Of Sugar Specific Degradation Enzymes In A Vector

Description

Given a vector of gene names that contain all sugar degradation enzymes from a genome of interest, count of number of different enzymes encoded by these genes that involve in the degradation of one specified sugar. Enzymes with same catalytic function (Reaction.EC) but encoded by different genes are counted once.

Usage

calculateStepsForOneSugar(geneVec, sugar, ER)

Arguments

geneVec	A vector of gene encoding sugar degradation enzymes.
sugar	The desired sugar degradation pathway. A simple sugar such as "fructose".
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

An integer. Number of different sugar specific enzymes present in the geneVec.

Examples

## Not run: 
 geneVec <- c("rpe", "rpiB", "eno", "fruK")
 ER <- EnzymaticReactions
 sugarScore <- calculateStepsForOneSugar(geneVec, "fructose", ER)
 sugarScore

## End(Not run)

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