R/combineBlocks.R

In David-J-R/BEclear: Correction of batch effects in DNA methylation data

#' combineBlocks
#'
#' @keywords internal
#'
#' @description  load and combine blocks
#'
#' @return the combined matrix consisting of the individual blocks
combineBlocks <- function(blockFrame, rowPos, colPos, dir) {
  D1 <- NULL
  blockCounter <- 1
  for (i in seq_len(rowPos[1])) {
    rowStart <- blockFrame[[2]][[blockCounter]]
    rowStop <- blockFrame[[3]][[blockCounter]]
    for (j in seq_len(colPos[1])) {
      colStart <- blockFrame[[4]][[blockCounter]]
      colStop <- blockFrame[[5]][[blockCounter]]
      ## special case, only one column block
      if (colPos[1] == 1) {
        blockName <- paste("D", blockCounter, sep = "")
        filename <- paste(blockName, "RData", sep = ".")
        file <- paste(dir, filename, sep = "/")
        load(file)
        assign(blockName, D1)
        frame <- D1
        currentRowGroup <- as.data.frame(frame)
        blockCounter <- blockCounter + 1
      } else {
        if (j == 1) {
          blockName <- paste("D", blockCounter, sep = "")
          filename <- paste(blockName, "RData", sep = ".")
          file <- paste(dir, filename, sep = "/")
          load(file)
          assign(blockName, D1)
          frame <- D1
          currentRowGroup <- as.data.frame(frame)
          blockCounter <- blockCounter + 1
        }
        else {
          blockName <- paste("D", blockCounter, sep = "")
          filename <- paste(blockName, "RData", sep = ".")
          file <- paste(dir, filename, sep = "/")
          load(file)
          assign(blockName, D1)
          frame <- D1
          currentRowGroup <- cbind(
            currentRowGroup,
            as.data.frame(frame)
          )
          blockCounter <- blockCounter + 1
        }
      }
    }
    ## special case, only one row block
    if (rowPos[1] == 1) {
      predictedGenes <- currentRowGroup
    } else {
      if (i == 1) {
        predictedGenes <- currentRowGroup
      }
      else {
        predictedGenes <- rbind(predictedGenes, currentRowGroup)
      }
    }
  }
  return(as.matrix(predictedGenes))
}