cmp_species_contributions: Evaluate species contributors for a single metabolite with...

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

Evaluate species contributors for a single metabolite with qPCR/species abundance data

Description

Evaluate species contributors for a single metabolite with qPCR/species abundance data

Usage

cmp_species_contributions(
  j,
  cmps_sub_good,
  all_rxns,
  subjects,
  norm_kos,
  ko_net,
  spec_abunds,
  ref_kos,
  cor_with = T
)

Arguments

j	metabolite # (usually from lapply/sapply)
cmps_sub_good	CMP scores for metabolites with abundance data
all_rxns	list of relevant reactions for each metabolite
subjects	vector of subjects
norm_kos	data.table of gene abundances
ko_net	network created by generate_genomic_network
spec_abunds	original species abundances
ref_kos	gene abundances for each species
cor_with	whether to look at the correlation of CMP scores of each species by itself with the metabolite, or of the whole community with that species removed

Value

List of length two. Item 1 is a table of all relevant species and correlation between the scores alone and the true scores, while item 2 is a vector of taxa that were classified as potential key taxa.

Examples

sapply(1:length(metabolites), cmp_species_contributions, cmp_scores, all_rxns,
all_subjects, ko_abunds, ko_net, spec_abunds, ref_kos)

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