get_spec_contribs: Perform a series of steps related to identifying...

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

Perform a series of steps related to identifying single-species contributors.

Description

Perform a series of steps related to identifying single-species contributors.

Usage

get_spec_contribs(
  contrib_file,
  data_dir,
  results_file,
  out_prefix,
  otu_id = "all",
  otu_file,
  valueVar = "singleMusicc",
  sum_to_genus,
  write_out = T,
  comparison = "cmps",
  met_data = "",
  taxonomy_file = "",
  var_share = F,
  cov_share = F,
  alreadyNormalized = F
)

Arguments

contrib_file	File where metagenome_contributions PICRUSt output is located
data_dir	Directory where OTU data is located
results_file	File where run_all_metabolites output is located
out_prefix	File path where output will be written too
otu_id	"All" to evaluate all detected OTUs, otherwise, a vector of OTU IDs to test for contribution
otu_file	OTU abundances file
valueVar	type of functional abundances to use for single species calculations - either "singleMusicc" or "RelAbundSample"
sum_to_genus	Whether to sum over OTUs to the genus level (requires Greengenes taxonomy info)
comparison	"mets" or "cmps"; whether to compare with community CMPs or metabolites themselves
met_data	Optional, metabolite concentration table if comparison = "mets"
var_share	If selected, will calculate variance share contributions instead of correlations
cov_share	If selected, will calculate covariance share contributions instead of correlations (cannot select both var and cov). Must provide metabolite concentration data.
alreadyNormalized	Don't re-normalize contribution table at all

Value

table of species, metabolites, whether that species is a contributor for that metabolite and the correlation strength

Examples

read_files(gene_file, met_file)

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