> For the complete documentation index, see [llms.txt](https://www.microbiomestat.wiki/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/incorporating-deseqdataset-into-microbiomestat.md).
# 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:
```r
# 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.
---
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