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fetching-data-from-mothur-into-microbiomestat.md

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description
Steps for importing Mothur-generated data into the MicrobiomeStat framework.

Importing Data from Mothur into MicrobiomeStat

This guide details the procedure to seamlessly import data generated by Mothur into the MicrobiomeStat environment.

{% file src="../../.gitbook/assets/esophagus.fn.list.gz" %} This compressed file contains the list file from Mothur, which typically encompasses OTU clustering information for various thresholds. {% endfile %}

{% file src="../../.gitbook/assets/esophagus.fn.shared.gz" %} The shared file provides a breakdown of the abundance of OTUs in each sample. {% endfile %}

{% file src="../../.gitbook/assets/esophagus.good.groups.gz" %} Group file indicating the sample assignment for each sequence. {% endfile %}

{% file src="../../.gitbook/assets/esophagus.tree.gz" %} Phylogenetic tree file representing the evolutionary relationships among OTUs. {% endfile %}

# Make sure the plyr package is installed
if (!require(plyr)) {
    install.packages("plyr")
    library(plyr)
} else {
    library(plyr)
}

# Specify the paths to your Mothur files
path_to_list_file <- "/path_to_your_files/esophagus.fn.list.gz"
path_to_group_file <- "/path_to_your_files/esophagus.good.groups.gz"
path_to_tree_file <- "/path_to_your_files/esophagus.tree.gz"
path_to_shared_file <- "/path_to_your_files/esophagus.fn.shared.gz"

# Import Mothur data into a MicrobiomeStat data object
data_obj <- mStat_import_mothur_as_data_obj(
    mothur_list_file = path_to_list_file,
    mothur_group_file = path_to_group_file,
    mothur_tree_file = path_to_tree_file,
    mothur_shared_file = path_to_shared_file
)

# After constructing data_obj, detach the plyr package to avoid conflicts with dplyr
if ("package:plyr" %in% search()) {
    detach("package:plyr", unload = TRUE)
    message("Detached plyr package to avoid potential conflicts with dplyr.")
}

The mStat_import_mothur_as_data_obj function facilitates the conversion of the Mothur dataset to the basic MicrobiomeStat data objects. Here are the key components:

  • mothur_list_file (Optional): Mothur-generated list file.
  • mothur_group_file (Optional): Group designation file from Mothur.
  • mothur_tree_file (Optional): Phylogenetic tree representation.
  • mothur_shared_file (Optional): OTU Abundance data across samples.
  • mothur_constaxonomy_file (Optional): Classification of OTUs at various taxonomic levels.
  • parseFunction (Optional): Custom function for taxonomy parsing, with 'parse_taxonomy_default' as an available option.

Structural overview of the `data_obj` generated after importing Mothur datasets into MicrobiomeStat.