> 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/integrating-data-from-dada2-into-microbiomestat.md).

# Importing Data from DADA2 into MicrobiomeStat

This guide will walk you through the steps required to import data from DADA2 into MicrobiomeStat.

### Download Necessary Files

{% file src="/files/oN0J7Ai73oTGK7XtlpS9" %}
Sequence table (`seq_tab`) - This table from DADA2 contains sample-specific sequence abundance data. Rows represent samples, and columns correspond to sequences.
{% endfile %}

{% file src="/files/bu9u6RmhiYzceAryDteE" %}
Taxonomy assignment table (`tax_tab`) - This table provides taxonomic classifications for sequences, helping users understand the biological context of the identified sequences.
{% endfile %}

{% file src="/files/an8U8diBkN7qSSUqNKK4" %}
Sample metadata table (\`sam\_tab\`) - This table offers detailed metadata for each sample, enriching the context and facilitating more in-depth analyses.
{% endfile %}

### Code to Import Data

```r
# This function requires the `Biostrings` and `yaml` packages.
 
# If you encounter issues when running the example code, please ensure that you have installed and loaded these packages.
library(Biostrings)
library(yaml)
# Read the sequence table from the downloaded RDS file
seq_tab <- readRDS("path_to_your_downloaded_folder/dada2_seqtab.rds")

# Read the taxonomy table from the downloaded RDS file
tax_tab <- readRDS("path_to_your_downloaded_folder/dada2_taxtab.rds")

# Read the sample metadata from the downloaded txt file
sam_tab <- read.table(
  "path_to_your_downloaded_folder/dada2_samdata.txt",
  sep = "\t",
  header = TRUE,
  row.names = 1
)

# Convert DADA2 data into a MicrobiomeStat data object
# phy_tree is optional: provide a phylogenetic tree (phylo object) if available
data_obj <- mStat_import_dada2_as_data_obj(
  seq_tab = seq_tab,
  tax_tab = tax_tab,
  sam_tab = sam_tab,
  phy_tree = NULL  # Set to a phylo object if you have a tree from DADA2
)
```

<figure><img src="/files/jzQbJKPJvMQicOly9sSC" alt=""><figcaption><p>Structure of the MicrobiomeStat data object after importing DADA2 data. This visualization highlights the different components of the data object, including the feature table, taxonomy table, and sample metadata, facilitating a comprehensive understanding of the imported dataset.</p></figcaption></figure>

{% hint style="info" %}
Note: Ensure to replace `"path_to_your_downloaded_folder"` with the actual path where you've saved the downloaded files.
{% endhint %}