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Aggregate Phyloseq Data by Taxonomic Level

Source: R/group_tax.R
group_tax.Rd

This function aggregates ASV data at specified taxonomic levels (e.g., Phylum, Class, Order, Family, or Genus) using the tax_glom function from the phyloseq package.

Usage

group_tax(
  physeq = rarefied_asv_physeq,
  norm_method = NULL,
  taxrank = c("Phylum", "Class", "Order", "Family", "Genus"),
  copy_correction = TRUE
)

Arguments

physeq

A phyloseq object containing the microbiome data. This is the input object that the function processes.

norm_method

A character string specifying the normalization method. Acceptable values are:

  • NULL: Use this option if no FCM or qPCR data is available, or if you wish to retain only relative abundances.

  • "fcm": Use this option if the data have been normalized using flow cytometry (FCM).

  • "qpcr": Use this option if the data have been normalized using quantitative PCR (qPCR).

taxrank

A character vector indicating the taxonomic levels at which to group the data.

Value

The function saves multiple phyloseq objects as RDS files. The aggregated objects are saved in the output directory output_data/rds_files/After_cleaning_rds_files/.

Details

The function applies the tax_glom function to group ASVs at each specified taxonomic level. It creates a dedicated folder for each taxonomic level under the output directory and saves the aggregated data as RDS files.

Examples

if (FALSE) { # \dontrun{
# Aggregate data using flow cytometry normalization
result <- group_tax(physeq = rarefied_asv_physeq, norm_method = "fcm")

# Aggregate data using qPCR normalization
result <- group_tax(physeq = rarefied_asv_physeq, norm_method = "qpcr")
} # }