get_species_cmp_scores: Updated version of getting all single-species CMP scores for...

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

Updated version of getting all single-species CMP scores for every compound and taxon

Description

Updated version of getting all single-species CMP scores for every compound and taxon

Usage

get_species_cmp_scores(
  species_table,
  network,
  normalize = T,
  relAbund = T,
  manual_agora = F,
  humann2 = F,
  leave_rxns = F,
  kos_only = F,
  remove_rev = T,
  fill_zeros = 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
leave_rxns	Return individual abundance/direction scores for each species and rxn
kos_only	Whether to call non-species-specific version of this function instead
remove_rev	Whether to remove reversible reactions before calculating anything
fill_zeros	Whether to consider samples with no relevant information on a metabolite as having 0 score (vs a missing value)

Value

data.table of cmp scores for each taxon and compound

Examples

get_species_cmp_scores(species_data, network)

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