R/calcBlockFrame.R

In uds-helms/BEclear: Correction of batch effects in DNA methylation data

#' calcBlockFrame
#'
#' @keywords internal
#'
#' @description  calculates every start and stop position for every block
#'
#' @return a data.frame containing the start and stop positions for each block
calcBlockFrame <-
  function(rowPositions,
             colPositions,
             rowBlockSize,
             colBlockSize) {
    ## construct data frame with all row-and column star-and stop positions
    blocks <- data.frame(
      number = numeric(),
      rowStartPos = numeric(),
      rowStopPos = numeric(),
      colStartPos = numeric(),
      colStopPos = numeric()
    )
    ## counters to choose the correct start - and stop positions within the
    ## loop
    rowCounter <- 1
    colCounter <- 1
    counter <- 1
    ## iteration over rows and columns to calculate the positions
    for (i in 0:(rowPositions[1] - 1)) {
      if (rowCounter < rowPositions[1] - 1) {
        currentRowStart <- i * rowBlockSize + 1
        currentRowStop <- i * rowBlockSize + rowBlockSize
        rowCounter <- rowCounter + 1
      } else {
        if (rowCounter == rowPositions[1] - 1) {
          currentRowStart <- rowPositions[2]
          currentRowStop <- rowPositions[4]
          rowCounter <- rowCounter + 1
        } else {
          if (rowCounter == rowPositions[1]) {
            currentRowStart <- rowPositions[3]
            currentRowStop <- rowPositions[5]
          }
        }
      }
      for (j in 0:(colPositions[1] - 1)) {
        if (colCounter < colPositions[1] - 1) {
          currentColStart <- j * colBlockSize + 1
          currentColStop <- j * colBlockSize + colBlockSize
          colCounter <- colCounter + 1
        } else {
          if (colCounter == colPositions[1] - 1) {
            currentColStart <- colPositions[2]
            currentColStop <- colPositions[4]
            colCounter <- colCounter + 1
          } else {
            if (colCounter == colPositions[1]) {
              currentColStart <- colPositions[3]
              currentColStop <- colPositions[5]
              colCounter <- 1
            }
          }
        }
        blocks <- rbind(
          blocks,
          data.frame(
            number = counter,
            rowStartPos = currentRowStart,
            rowStopPos = currentRowStop,
            colStartPos = currentColStart,
            colStopPos = currentColStop
          )
        )
        counter <- counter + 1
      }
    }
    return(blocks)
  }