R/format.R

In isglobal-brge/GCCA: Generalized Canonical Correlation Analysis having missing individuals

#' Formats a character matrix into a numeric matrix (used for the methylation assay)
#' @param index indicates in which position from the list is the matrix
#' @export

matrix.chr2num <- function(listMAE, index) {

  # Check that the input is of ListMAE class
  if (!class(listMAE) == "ListMAE")
    stop("Input must be a 'ListMAE' object \n")

  # Check index parameter has been given
  if (missing(index))
    stop("Index parameter indicating the position of the matrix in the list must be given \n")

  # First, keep rownames and colnames from the original matrix
  chr.colnames <- colnames(listMAE[[index]])
  chr.rownames <- rownames(listMAE[[index]])
  chr.numeric <- as.numeric(listMAE[[index]])
  # Create new matrix with the same values and dimensions of the original matrix. By default, values will be numeric.
  num.matrix <- matrix(data=chr.numeric, ncol=dim(listMAE[[index]])[2],
              nrow=dim(listMAE[[index]])[1])
  # Reassign colnames and rownames from the original matrix
  colnames(num.matrix) <- chr.colnames
  rownames(num.matrix) <- chr.rownames
  # Update the matrix in the list
  listMAE[[index]] <- num.matrix
  listMAE
}