gene_contributions: Identify potential important gene contributors for each...

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Identify potential important gene contributors for each metabolite.

Description

Identify potential important gene contributors for each metabolite.

Usage

gene_contributions(j, cmps_sub_good, all_rxns, subjects, norm_kos, ko_net)

Arguments

j	index (from lapply usually)
cmps_sub_good	CMP scores for metabolites to be analyzed
all_rxns	list of reaction tables for each compound
subjects	vector of subject names
norm_kos	gene abundance matrix
ko_net	full network

Value

list of information on contributors. Item 1 is the table of correlations between scores with and without each gene (also written to a file). Item 2 is a table of the associated reactions for each of the contributor genes. Item 3 is an integer equal to 1 if the metabolite scores are predicted primarily by synthesis, -1 if scores are predicted primarily by degradation, or 0 if neither. Item 4 is a vector of the number of genes and contributor genes involved in synthesis and degradation reactions.

Examples

lapply(1:length(good_mets), cmp_contributions, cmps_sub_good = cmps_sub_good, all_rxns = all_rxns[[j]],
subjects=subjects, norm_kos = norm_kos, ko_net = ko_net)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.