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
seq_tab
) - This table from DADA2 contains sample-specific sequence abundance data. Rows represent samples, and columns correspond to sequences.tax_tab
) - This table provides taxonomic classifications for sequences, helping users understand the biological context of the identified sequences.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
)

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