var_shares_cmps: Get variance share contributions to CMP scores for all...

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

Get variance share contributions to CMP scores for all compounds

Description

Get variance share contributions to CMP scores for all compounds

Usage

var_shares_cmps(
  cmps_sub_good,
  all_rxns,
  subjects,
  norm_kos,
  ko_net,
  all_taxa,
  single_spec_cmps,
  contrib_threshold = 0.45,
  cov_shares = F,
  met_data = NULL
)

Arguments

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
contrib_threshold	Threshold for binary contribution
cov_shares	Whether to calculate contribution to covariance with mets instead of variance (requires supplying metabolite data)
met_data	Metabolite concentration data (if calculating contribution to covariance)
scaled_pos_contrib	Whether to use scaled positive contributions

Value

data.table of variance contributions to CMP scores

Examples

var_shares_cmps(cmps_total, all_rxns, subjects, norm_kos, ko_net, all_taxa, single_spec_cmps, contrib_threshold)

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