> 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/transferring-data-from-biom-into-microbiomestat.md).

# Importing Data from BIOM into MicrobiomeStat

Follow the instructions below to convert your BIOM data into a format suitable for MicrobiomeStat.

{% file src="/files/NPcN1gJ5lkm1STQUF9Gk" %}
BIOM file containing biological observation matrix and associated metadata.
{% endfile %}

{% file src="/files/7l4CyPkzQtmyHzbdXoRa" %}
Phylogenetic tree file representing evolutionary relationships among observed species.
{% endfile %}

{% code fullWidth="true" %}

```r
# Example code

# Specify the path to your BIOM data. Replace the placeholder with the correct path on your system.
rich_dense_biom <- "rich_dense_otu_table.biom"
# Reminder: Ensure that you replace the above path with the actual location of your BIOM file.

# Specify the path to your phylogenetic tree. Again, replace the placeholder with the correct path on your system.
treefilename <- "biom-tree.phy"
# Reminder: Ensure that you replace the above path with the actual location of your phylogenetic tree file.

# Convert the BIOM data and associated phylogenetic tree (if provided) 
# into a format suitable for MicrobiomeStat using the mStat_import_biom_as_data_obj function.
data.obj <- mStat_import_biom_as_data_obj(BIOMfilename = rich_dense_biom, treefilename = treefilename)

# The resulting 'data.obj' is now a MicrobiomeStat data object that you can use for further analyses.
```

{% endcode %}

<figure><img src="/files/U1RoobP855fdXTIoaPBt" alt=""><figcaption><p>Structure of the MicrobiomeStat data object created from BIOM data.</p></figcaption></figure>

By employing the `mStat_import_biom_as_data_obj` function, the BIOM data, along with optional phylogenetic tree data, can be integrated into the MicrobiomeStat framework. Here's a brief overview of the function's parameters:

* **BIOMfilename**: The file path to your BIOM data.
* **treefilename** (Optional): The file path to your phylogenetic tree.
* **parseFunction** (Optional): A user-defined function to interpret the taxonomy from the BIOM file metadata.