get_all_singleSpec_cmps: Get single-species CMP scores for every OTU and metabolite

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

Get single-species CMP scores for every OTU and metabolite

Description

Get single-species CMP scores for every OTU and metabolite

Usage

get_all_singleSpec_cmps(
  all_otus,
  all_koAbunds_byOTU,
  valueVar,
  out_prefix,
  rxn_table,
  degree_filter = 30,
  write_out = T,
  normalize = T,
  ko_net = ""
)

Arguments

all_otus	vector of OTUs or taxa
all_koAbunds_byOTU	list of KO abundances for each OTU
valueVar	"relAbundSample" or "singleMusicc", abundance metric to use for single taxon gene abundances
out_prefix	Path of directory for loading and saving output
rxn_table	Community network template
degree_filter	Filter compounds connected to more than this number of KOs in the metabolic network model (default 30)
write_out	Whether to save output
normalize	Whether to normalize rows when making the network EMM
ko_net	Optional, community network model. if provided the function will not generate one for this specific species.

Value

list of matrices of cmp scores for each taxon

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