R/read_amp.R

In michbur/dpcR: Digital PCR Analysis

read_zipped_amps <- function(file) {
  files_names <- unzip(file, list = TRUE)[["Name"]]
  amp_files <- files_names[grep("Amplitude", files_names)]

  wells <- sapply(strsplit(amp_files, "_"), function(i) i[length(i) - 1])
  s_well <- sort(wells)

  raw_status <- do.call(rbind, lapply(amp_files[order(wells)], function(single_file) {
    n_clust <- tabulate(read.table(unz(file, single_file),
      sep = ",", dec = ".",
      nrows = 25000, header = TRUE,
      colClasses = "numeric"
    )[["Cluster"]])
    if (length(n_clust) != 4) {
      n_clust <- c(n_clust, rep(0, 4 - length(n_clust)))
    }
    n_clust
  }))

  dat_summ <- data.frame(
    x = substr(s_well, 0, 1),
    y = as.numeric(sub("[A-Z]", "", s_well)),
    channel = c(rep(1, length(wells)), rep(2, length(wells))),
    positives = c(rowSums(raw_status[, 2L:3]), rowSums(raw_status[, 3L:4])),
    negatives = c(rowSums(raw_status[, c(1, 4)]), rowSums(raw_status[, 1L:2]))
  )

  dat_summ[["k"]] <- dat_summ[["positives"]]
  dat_summ[["n"]] <- dat_summ[["positives"]] + dat_summ[["negatives"]]
  dat_summ[, c("x", "y", "channel", "k", "n")]
}

amp2dpcr <- function(x) {
  col_names <- 1L:12
  names(col_names) <- LETTERS[1L:8]

  create_adpcr(
    data = matrix(x[["k"]], nrow = 1), n = x[["n"]],
    exper = 1L:nrow(x), replicate = rep(1, nrow(x)), type = "tnp",
    assay = paste0("ch", x[["channel"]]),
    col_names = LETTERS[1L:8],
    row_names = as.character(1L:12),
    row_id = x[["y"]],
    col_id = col_names[x[["x"]]],
    panel_id = factor(paste0("ch", x[["channel"]])), threshold = 1
  )
}