prioritize: Rank metabolic features and prioritize based on predicted...

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

Rank metabolic features and prioritize based on predicted bioactivity.

Description

Metabolic features are ranked based on AVA, and q-value and effect size of differential abundance. The harmonic mean of these three ranks is calculated and used as the meta-rank to prioritize potentially bioactive features in a phenotype (or condition). Top-ranked features have good relative abundance, and are significantly perturbed in the specified environment/phenotype.

Usage

prioritize(se, mod.assn, mac.ava, mac.qval, mac.es)

Arguments

se	SummarizedExperiment object created using Macarron::prepInput()
mod.assn	the output of Macarron::findMacMod()
mac.ava	the output of Macarron::calAVA()
mac.qval	the output of Macarron::calQval()
mac.es	the output of Macarron::calES()

Value

mac.result - metabolic features listed according to priority

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)                         

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