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Convert Phyloseq Data to Tibble and Export by Taxonomic Level

Source: R/psdata_to_tibble.R
psdata_to_tibble.Rd

This function transforms a phyloseq object into a tibble for each specified taxonomic level using the psmelt function from the phyloseq package.

Usage

psdata_to_tibble(
  physeq = rarefied_genus_physeq,
  norm_method = NULL,
  taxrank = c("Phylum", "Class", "Order", "Family", "Genus")
)

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-derived tibbles as RDS files and returns a list of tibbles:

  • If norm_method is NULL: A tibble of copy number–corrected counts is saved as <project_name>_psmelt_<tax>_level_copy_number_corrected_counts.rds for each taxonomic level.

    \item **If \code{norm_method = "fcm"}:**
      Two tibbles are saved for each taxonomic level:
      \itemize{
        \item A tibble of copy number–corrected counts.
        \item A tibble of FCM-normalized, rarefied counts saved as
              \code{<project_name>_psmelt_<tax>_level_fcm_normalised_cell_concentration_rarefied.rds}.
      }

\item **If \code{norm_method = "qpcr"}:**
      Two tibbles are saved for each taxonomic level:
      \itemize{
        \item A tibble of copy number–corrected counts.
        \item A tibble of qPCR-normalized, rarefied counts saved as
              \code{<project_name>_psmelt_<tax>_level_qpcr_normalised_cell_concentration_rarefied.rds}.
      }

Details

The primary task of this function is to convert a phyloseq object into a tibble at each specified taxonomic level using the psmelt function.

Examples

if (FALSE) { # \dontrun{
  # Export data without normalization (copy number–corrected counts only)
  result <- psdata_to_tibble(physeq = rarefied_genus_physeq)

  # Export data with flow cytometry normalization
  result <- psdata_to_tibble(physeq = rarefied_genus_physeq, norm_method = "fcm")

  # Export data with qPCR normalization
  result <- psdata_to_tibble(physeq = rarefied_genus_physeq, norm_method = "qpcr")
} # }