get_cmp_summary: Get summary of CMP score basis across all samples

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

Get summary of CMP score basis across all samples

Description

Get summary of CMP score basis across all samples

Usage

get_cmp_summary(
  species_table,
  network,
  normalize = T,
  relAbund = T,
  manual_agora = F,
  humann2 = F,
  kos_only = F,
  remove_rev = T,
  met_subset = NULL,
  contrib_sizes = NULL,
  return_var_shares = T
)

Arguments

species_table	OTU abundance table (wide format)
network	Species-specific network table, product of build_network functions
normalize	Whether to normalize rows when making the network EMM
relAbund	Whether to use relative abundance normalization
manual_agora	Whether the metabolite are already specified using AGORA/BiGG (and therefore should not be mapped back to KEGG)
humann2	Whether the species data is long-form humann2 gene-species abundances
kos_only	Whether to call non-species-specific version of this function instead
remove_rev	Whether to remove reversible reactions before calculating anything
met_subset	Subset of metabolites to keep
contrib_sizes	Contribution values to order by, if applicable
return_var_shares	Whether to also return contributions table with summary information

Value

List of tables of stats on relevant nonzero species and reactions in the network for each compound

Examples

get_cmp_summary(species, network)

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