Converting SummarizedExperiment into MicrobiomeStat

A step-by-step guide on converting SummarizedExperiment data format for compatibility with MicrobiomeStat.

The Bioconductor package SummarizedExperiment provides a convenient representation of experimental data. MicrobiomeStat provides a straightforward method for converting SummarizedExperiment objects.

# Check if the 'airway' package is installed
if (!requireNamespace("airway", quietly = TRUE)) {
  # If not installed, install 'airway'
  BiocManager::install("airway")
}

# Load necessary libraries
library(airway)

# Use the provided 'airway' dataset as an example
data(airway)

# Convert the SummarizedExperiment object 'airway' into a MicrobiomeStat data object
airway_obj <- mStat_convert_SummarizedExperiment_to_data_obj(airway)

Structure of the airway_obj data object, converted from the airway SummarizedExperiment dataset. The visualization showcases the primary components of the MicrobiomeStat data object, detailing its matrices and data frames derived from the original dataset.

The function mStat_convert_SummarizedExperiment_to_data_obj requires:

• se.obj: A SummarizedExperiment object for conversion.

Post conversion, the data is organized into a MicrobiomeStat data object with the following components:

• feature.tab: A matrix derived from assay data.

• feature.ann: A matrix consisting of rowData or feature annotations. Only the features present in the assay data are retained.

• meta.dat: A data frame containing colData or sample metadata.

For efficient analysis, features with an aggregate count of zero in the assay data are excluded during the conversion process.