Converting MRExperiment into MicrobiomeStat

If your data is stored in a MRExperiment object from the metagenomeSeq package, the mStat_convert_MRExperiment_to_data_obj() function provides a direct conversion to the MicrobiomeStat data format.

Function Overview

mStat_convert_MRExperiment_to_data_obj(mr.obj)

Parameters:

• mr.obj: A MRExperiment object to be converted.

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

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

• meta.dat: A data frame of sample metadata

• feature.ann: A matrix of feature annotations (if available)

Example Usage

library(metagenomeSeq)

# Load example data from metagenomeSeq
data(mouseData)

# Convert to MicrobiomeStat format
data.obj <- mStat_convert_MRExperiment_to_data_obj(mouseData)

# 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 metagenomeSeq package to be installed.

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