Importing Data from DADA2 into MicrobiomeStat

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

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

Download Necessary Files

11KB

dada2_seqtab.rds

9KB

dada2_taxtab.rds

397B

dada2_samdata.txt

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.

Note: Ensure to replace "path_to_your_downloaded_folder" with the actual path where you've saved the downloaded files.