incorporating-deseqdataset-into-microbiomestat.md

description
A guide on converting DESeqDataSet data format into the MicrobiomeStat format.

Converting DESeqDataSet into MicrobiomeStat

This guide provides the recipe for converting the DESeqDataSet format to MicrobiomeStat format.

To begin, let's inspect the initial structure of our DESeqDataSet data:

Initial structure of the DESeqDataSet data.

Proceed with the steps below to conduct the conversion:

# Example Code (replace with your real dataset!)
# Load necessary packages
 library(airway)
 library(DESeq2)

# Load dataset
 data("airway")
 dds <- DESeqDataSet(airway, design = ~ cell + dex)

# Convert DESeqDataSet to MicrobiomeStat data object
 data.obj <- mStat_convert_DESeqDataSet_to_data_obj(dds)

Upon conversion, the data structure will be transformed as follows:

Structure of the MicrobiomeStat data object after importing DESeqDataSet data.

The mStat_convert_DESeqDataSet_to_data_obj function facilitates the transition:

• dds.obj: The DESeqDataSet object slated for conversion.

After the conversion, the MicrobiomeStat data object consists of:

• feature.tab: A matrix containing count data.
• meta.dat: A data frame detailing the sample information.
• feature.ann: A matrix presenting feature annotations.

For data integrity and relevance, the function ensures only features with a sum > 0 from the counts data are retained.