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Create a Phyloseq Object

Source: R/creating_physeq_object.R
creating_physeq_object.Rd

This function creates a phyloseq object using input data files such as feature tables, taxonomic assignments, phylogenetic tree, and unified metadata into a single phyloseq object for downstream analysis.

Usage

creating_physeq_object(projects)

Arguments

projects

A character vector containing the names of the project (folders).

Value

A phyloseq object that integrates feature tables, taxonomy, phylogenetic trees, and metadata. This object is also saved as an RDS file for further usage in downstream analyses.

Details

This function performs the following steps:

  • Defines the paths to the required input files (feature table, rooted tree, taxonomy, and metadata).

  • Searches for and retrieves these files from the input_data directory.

  • Calls the qza_to_phyloseq() function from the qiime2R package to generate a phyloseq object based on the provided input files.

  • Adds read count information to the sample metadata within the phyloseq object.

The function assumes the following files are present in the input_data directory:

  • table.qza: Feature table containing sample feature data.

  • rooted-tree.qza: Phylogenetic tree.

  • classifier.qza: Taxonomic classification file.

  • metadata_formatted.tsv: Unified sample metadata.

The resulting phyloseq object is essential for downstream analyses and integrates all input files into a single, structured object. The created phyloseq object is saved as an RDS file named <project_name>_phyloseq_uncleaned.rds in the output_data/rds_files/Before_cleaning_rds_files directory.

Examples

if (FALSE) { # \dontrun{
# Example usage:
physeq_object <- creating_physeq_object(projects)
} # }