Converting MultiAssayExperiment into MicrobiomeStat

If your data is stored in a MultiAssayExperiment object (commonly used in multi-omics studies), the mStat_convert_MultiAssayExperiment_to_data_obj() function converts a specified experiment to the MicrobiomeStat data format.

Function Overview

mStat_convert_MultiAssayExperiment_to_data_obj(mae.obj, experiment_name = NULL)

Parameters:

• mae.obj: A MultiAssayExperiment object to be converted.

• experiment_name: A string specifying which experiment in the MultiAssayExperiment to convert. Default is the first experiment.

Returns: A MicrobiomeStat data object (a list) containing:

• feature.tab: A matrix of assay data (features as rows, samples as columns)

• meta.dat: A data frame of sample metadata (from colData)

Example Usage

library(MultiAssayExperiment)

# Assuming 'mae' is your MultiAssayExperiment object
# Convert the "16S" experiment to MicrobiomeStat format
data.obj <- mStat_convert_MultiAssayExperiment_to_data_obj(mae, "16S")

# Or convert the first experiment (default)
data.obj <- mStat_convert_MultiAssayExperiment_to_data_obj(mae)

# Verify the conversion
print(dim(data.obj$feature.tab))
print(head(data.obj$meta.dat))

Notes

• Only features with a sum > 0 across all samples are retained during conversion.

• The function requires the MultiAssayExperiment package to be installed.

• After conversion, validate the data object with mStat_validate_data(data.obj).