ezclean: Clean and Process Microbiome Data

In mbX: A Comprehensive Microbiome Data Processing Pipeline

Clean and Process Microbiome Data

Description

Processes microbiome and metadata files (e.g., 16S rRNA sequencing data) to produce an analysis-ready dataset. Supports CSV, TXT, and 'Excel' file formats. This function validates file formats, reads the data, and merges the datasets by the common column 'SampleID'. If a 'Taxonomy' column exists, the data are filtered to include only rows matching the provided taxonomic level.

Usage

ezclean(microbiome_data, metadata, level = "d")

Arguments

microbiome_data	A string specifying the path to the microbiome data file.
metadata	A string specifying the path to the metadata file.
level	A string indicating the taxonomic level for filtering the data (e.g., "genus").

Value

A data frame containing the cleaned and merged dataset.

Examples

  # Example usage (ensure that 'inst/extdata' contains the appropriate files,
  # or modify this example to use your own data)
  microbiome_data <- system.file("extdata", "microbiome.csv", package = "mbX")
  metadata <- system.file("extdata", "metadata.csv", package = "mbX")
  if (nzchar(microbiome_data) && nzchar(metadata)) {
    cleaned_data <- ezclean(microbiome_data, metadata, "genus")
    head(cleaned_data)
  } else {
    message("Sample data files not found.")
  }

mbX documentation built on April 3, 2025, 8:59 p.m.