showBest: View highly prioritized bioactives grouped by modules.

In biobakery/Macarron: Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

View highly prioritized bioactives grouped by modules.

Description

Modules are listed in the order of priority. Only the top-ranked n features in each module are shown. The priority of a module is the ratio of number of features in it that are ranked higher than the cut-off and the size of the module. This utility function makes it easier to understand default prioritization results of large datasets where a few hundred metabolic features are highly-prioritized.

Usage

showBest(
  mac.result,
  priority_threshold = 0.9,
  per_module = 10,
  per_phenotype = 1000,
  only_characterizable = TRUE
)

Arguments

mac.result	the output of Macarron::Macarron() or Macarron::prioritize().
priority_threshold	cut-off of priority score. Default = 0.9.
per_module	show first n highly prioritized features in a module. Default = 10
per_phenotype	show highly prioritized n features per phenotype/condition. Default = 1000
only_characterizable	show highly prioritized features in modules which contain at least one annotated metabolite. Default = TRUE

Value

best.mets -highly-prioritized bioactives in each module in each phenotype

Examples

prism_abundances = system.file("extdata", "demo_abundances.csv", package="Macarron")
abundances_df = read.csv(file = prism_abundances, row.names = 1)
prism_annotations = system.file("extdata", "demo_annotations.csv", package="Macarron")
annotations_df = read.csv(file = prism_annotations, row.names = 1)
prism_metadata = system.file("extdata", "demo_metadata.csv", package="Macarron")
metadata_df = read.csv(file = prism_metadata, row.names = 1)
met_taxonomy = system.file("extdata", "demo_taxonomy.csv", package="Macarron")
taxonomy_df = read.csv(file = met_taxonomy)
mbx <- Macarron::prepInput(input_abundances = abundances_df,
                            input_annotations = annotations_df,
                            input_metadata = metadata_df)
w <- Macarron::makeDisMat(se = mbx)
modules.assn <- Macarron::findMacMod(se = mbx, 
                                     w = w,
                                     input_taxonomy = taxonomy_df)
mets.ava <- Macarron::calAVA(se = mbx,
                             mod.assn = modules.assn)                                     
mets.qval <- Macarron::calQval(se = mbx,
                               mod.assn = modules.assn)
mets.es <- Macarron::calES(se = mbx,
                           mac.qval = mets.qval)
mets.prioritized <- Macarron::prioritize(se = mbx,
                                         mod.assn = modules.assn,
                                         mac.ava = mets.ava,
                                         mac.qval = mets.qval,
                                         mac.es = mets.es)  
best.mets <- Macarron::showBest(mac.result = mets.prioritized)
                                                                

biobakery/Macarron documentation built on June 29, 2024, 7:58 a.m.