calES: Calculate effect size of differential abundance of metabolic...

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

Calculate effect size of differential abundance of metabolic features.

Description

Effect size of a metabolic feature is the difference in mean log2 transformed abundances in test and control (reference) samples. For the specified metadata variable, effect size is calculated for all test categories against the reference category.

Usage

calES(se, mac.qval)

Arguments

se	SummarizedExperiment object created using Macarron::prepInput().
mac.qval	the output of Macarron::calQval().

Value

mac.es effect sizes of metabolic features in phenotypes of interest.

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.qval <- Macarron::calQval(se = mbx,
                               mod.assn = modules.assn)
mets.es <- Macarron::calES(se = mbx,
                           mac.qval = mets.qval)                               

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