findPerturbMet: Identify perturbed metabolites based on changes in the...

In yuliangwang/perturb.met: What the Package Does (One Line, Title Case)

Description

Identify perturbed metabolites based on changes in the relative expression of enzymes around a metabolite

Usage

findPerturbMet(expression_data, mets2genes, expressed_threshold)

Arguments

expression_data	data frame of the input expression data.First column must be gene symbol; second column is the expression level in reference condition; third comun is the expression level in treated/perturbed condition; expression in TPM or FPKM, not log transformed.
mets2genes	data frame that describe gene-metabolite connections. It includes two columns: "met", which lists metabolite symbols; and "genes" which include gene symbols for genes that produce or consume the corresponding metabolite
expressed_threshold	a value above which a gene is considered expressed

Value

a list that has two components. 1. perturbed_mets: list of perturbed metabolites sorted by p-value; 2. met_gene_pairs: metabolite-gene pairs after filtering down to expressed genes and their connected metabolites;

yuliangwang/perturb.met documentation built on Jan. 21, 2021, 12:27 a.m.