cmp_species_contributions_picrust: 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 OTU and PICRUSt data, typically called by get_spec_contribs

Description

Evaluate species contributors for a single metabolite with OTU and PICRUSt data, typically called by get_spec_contribs

Usage

cmp_species_contributions_picrust(
  j,
  cmps_sub_good,
  all_rxns,
  subjects,
  norm_kos,
  ko_net,
  all_taxa,
  single_spec_cmps,
  cor_with = T,
  comparison = "cmps",
  met_data = ""
)

Arguments

j	metabolite ID # (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
all_taxa	vector of OTUs
single_spec_cmps	single-species CMP scores calculated from get_spec_contribs function
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
comparison	"mets" or "cmps"; whether to compare with community CMPs or metabolites themselves
met_data	Optional, metabolite concentration table if comparison = "mets"

Value

list of 2-item lists for every metabolite - 1st item is data.table of OTUs and correlations, second item is vector of OTUs with correlations > 0.5

Examples

lapply(1:length(metabolites), cmp_species_contributions_picrust, 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.