R/uniqueSeqs.R

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

#' Unique sequences
#'
#' Aggregates all productive sequences within a list of data frames by
#' duplicate_count.
#'
#' @param productive_table A tibble of productive amino acid sequences
#' imported using the function LymphoSeq2 function [productiveSeq()] where the
#' aggregate parameter was set to "junction_aa".
#' @param unique_type Use `"junction_aa"` (the default) to aggregate by amino
#'  acid sequences. Use `"junction"` to aggregate by nucleotide sequences.
#' @return A data frame of unique amino acid sequences from the list of
#' data frames aggregated by "duplicate_count".
#' @examples
#' file_path <- system.file("extdata", "TCRB_sequencing",
#'  package = "LymphoSeq2")
#' study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
#' study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
#' amino_table <- LymphoSeq2::productiveSeq(study_table = study_table,
#'  aggregate = "junction_aa")
#' unique_seqs <- LymphoSeq2::uniqueSeqs(productive_table = amino_table,
#'  unique_type = "junction_aa")
#' @export
uniqueSeqs <- function(productive_table = productive_table,
                       unique_type = "junction_aa") {
  # Add checks to see if the tibble is a productive table
  unique_seq <- tibble::tibble()
  if (unique_type == "junction") {
    unique_seq <- productive_table |>
      dplyr::group_by(junction) |>
      dplyr::summarize(duplicate_count = sum(duplicate_count)) |>
      dplyr::arrange(desc(duplicate_count))
  } else if (unique_type == "junction_aa") {
    unique_seq <- productive_table |>
      dplyr::group_by(junction_aa) |>
      dplyr::summarize(duplicate_count = sum(duplicate_count)) |>
      dplyr::arrange(desc(duplicate_count))
  }
  return(unique_seq)
}