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integrating-data-from-dada2-into-microbiomestat.md

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Learn the steps to import data from DADA2 into MicrobiomeStat's data structure.

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="../../.gitbook/assets/dada2_seqtab.rds" %} 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="../../.gitbook/assets/dada2_taxtab.rds" %} 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="../../.gitbook/assets/dada2_samdata.txt" %} 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

# 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
data_obj <- mStat_import_dada2_as_data_obj(
  seq_tab = seq_tab,
  tax_tab = tax_tab,
  sam_tab = sam_tab
)

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.

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