ourMELONS/R/computeDiffInCounts.R

computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
  # % Muodostaa max_noalle*nloci taulukon, jossa on niiden alleelien
  # % lukum<75><6D>r<EFBFBD>t (vastaavasti kuin COUNTS:issa), jotka ovat data:n
  # % riveill<6C> rows. rows pit<69><74> olla vaakavektori.

  diffInCounts <- zeros(max_noalle, nloci)
  for (i in seq_len(nrow(data))) {
    row <- data[i, ]
    notEmpty <- as.matrix(matlab2r::find(row >= 0))

    if (length(notEmpty) > 0) {
      diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] <-
        diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] + 1
    }
  }
  diffInCounts <- matrix(
    data = diffInCounts[!is.na(diffInCounts)],
    nrow = max_noalle,
    ncol = nloci,
    byrow = TRUE
  )
  return(diffInCounts)
}