Overwrite matrix as default

[Alexander Tedeschi]

Suggestion to change the default mode to overwrite, or to create a parameter that specifies write mode as "append" or "overwrite". As it is, WriteMatrixToFile silently appends if the filename is the same.

WriteMatrixToFile <- function (tmpMatrix, tmpFileName, blnRowNames, blnColNames) 
{
    output <- file(tmpFileName, "at")  # change "at" to "wt" 
    utils::write.table(tmpMatrix, output, sep = "\t", quote = FALSE, 
        row.names = blnRowNames, col.names = blnColNames)
    close(output)
}

If we follow the multiClust vignette, for example:

> WriteMatrixToFile(tmpMatrix=data.log,
+                   tmpFileName="GSE2034.normalized.expression.txt",
+                   blnRowNames=TRUE, blnColNames=TRUE)
> data.exprs <- input_file(input="GSE2034.normalized.expression.txt")
[1] "The gene expression matrix has been loaded"
> dim(data.exprs)
[1] 22283   286
> WriteMatrixToFile(tmpMatrix=data.log,
+                   tmpFileName="GSE2034.normalized.expression.txt",
+                   blnRowNames=TRUE, blnColNames=TRUE)
> data.exprs <- input_file(input="GSE2034.normalized.expression.txt")
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed