mbX (version 0.2.0)

ezclean: 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")

Value

A data frame containing the cleaned and merged dataset.

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").

Examples

if (FALSE) {
  mb  <- system.file("extdata", "microbiome.csv", package = "mbX")
  md  <- system.file("extdata", "metadata.csv",   package = "mbX")
  if (nzchar(mb) && nzchar(md)) {
    cleaned_data <- ezclean(mb, md, "g")
    head(cleaned_data)
  } else {
    message("Sample data files not found.")
  }
}