completenessForAllPathways: Evaluate The Completeness Of All Sugar Degradation Pathways

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

Evaluate The Completeness Of All Sugar Degradation Pathways

Description

Given a genome of interest, described by genomeName and a vector of sugar degradation genes, evaluate the completeness of all sugar degradation pathways. The completeness is evaluated by (steps can be catalyzed) over (total steps within a pathway), and this score should always be between 0 and 1 (inclusive).

Usage

completenessForAllPathways(geneVec, allSugars, ER, totalSteps)

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.
totalSteps	A vector containing counts of total steps for all sugar degradation pathways. Result of helper function calculateTotalStepsForAllSugars

Value

A named vector containing completeness score for all sugar degradation pathways.

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