R/get_mappgene_data.R

In jeffkimbrel/MappgeneSummary: Summarize Mappgene SNV Data

#' Load the mappgene data into a tibble
#'
#' @param path The path to the folder with the .ivar.snpSIFT.txt and .ivar.lofreq.snpSIFT.txt files.
#' @param workflow The mappgene workflow type(s). Accepts a single string, or a vector of both "ivar" and "lofreq".
#' @param sample_cleanup Additional text to remove from the sample names.
#'
#' @export
#'

read_mappgene_data <- function(path, workflow = c("ivar", "lofreq"), sample_cleanup = "LLNL_") {
  if (length(setdiff(workflow, c("ivar", "lofreq"))) > 0) {
    stop("Sorry, there are workflow terms I don't recognize. Please use lofreq and/or ivar only")
  }

  l <- list()

  if ("ivar" %in% workflow) {
    pattern <- "*.ivar.snpSIFT.txt$"

    files <- list.files(path = path, pattern = pattern, recursive = TRUE, full.names = T)
    message(paste("Found", length(files), "ivar files"))

    ivar <- sapply(files,
      readr::read_delim,
      delim = "\t",
      comment = "##",
      simplify = FALSE,
      col_types = "ficcdifffcciic"
    ) |>
      lapply(\(x) dplyr::mutate(x, dplyr::across(ALT_QUAL, as.double))) |> # to fix when a file is empty
      dplyr::bind_rows(.id = "id")

    ivar <- ivar |>
      dplyr::filter(ALT_QUAL > 20) |>
      dplyr::filter(FILTER == "PASS")

    l$ivar <- ivar
  }

  if ("lofreq" %in% workflow) {
    pattern <- "*.ivar.lofreq.snpSIFT.txt$"

    files <- list.files(path = path, pattern = pattern, recursive = TRUE, full.names = T)
    message(paste("Found", length(files), "lofreq files"))

    lofreq <- sapply(files,
      readr::read_delim,
      delim = "\t",
      comment = "##",
      simplify = FALSE,
      col_types = "ficcdifffcciic"
    ) |>
      # lapply(\(x) mutate(x, across(ALT_QUAL, as.double))) |> # to fix when a file is empty
      dplyr::bind_rows(.id = "id")
    l$lofreq <- lofreq
  }

  df <- dplyr::bind_rows(l, .id = "PIPELINE") |>
    dplyr::mutate(FILE = basename(id)) |>
    dplyr::select(-id) |>
    dplyr::mutate(SAMPLE = FILE) |>
    dplyr::mutate(SAMPLE = stringr::str_replace(SAMPLE, ".ivar.snpSIFT.txt", "")) |>
    dplyr::mutate(SAMPLE = stringr::str_replace(SAMPLE, ".ivar.lofreq.snpSIFT.txt", "")) |>
    dplyr::mutate(SAMPLE = stringr::str_replace(SAMPLE, sample_cleanup, ""))

  names(df) <- gsub(x = names(df), pattern = "ANN\\[\\*\\]\\.", replacement = "")

  df <- df |>
    dplyr::select(
      "SAMPLE", "PIPELINE", "GENE", "FEATUREID", "POS", "REF", "ALT", "AF", "DP", "EFFECT",
      "HGVS_C", "HGVS_P", "CDNA_POS", "AA_POS", "FILE"
    ) |>
    unique() |>
    dplyr::mutate(ALT_DP = as.integer(DP * AF)) |>
    tibble::as_tibble()

  return(df)
}