R/IO.R

In ge11232002/NGS: Next Generation Sequencing Data Analysis

### -----------------------------------------------------------------
### More friendly write.table
### Not exported!
my.write.table = function(values, file=file, head="Identifier", row.names=TRUE, col.names=TRUE,
                          append=FALSE, quote=FALSE, sep="\t", na="NA", digits=NA){
  
  if (is.vector(values)){
    values = as.data.frame(values)
  }
  
  if (!is.na(digits)){
    if (is.data.frame(values)){
      for (i in 1:length(values)){
        if (is.numeric(values[[i]])){
          isInteger = as.integer(values[[i]]) == values[[i]]
          isInteger[is.na(isInteger)] = TRUE
          if (any(!isInteger)){
            values[[i]] = signif(values[[i]], digits=digits)
          }
        }
      }
    } else {
      if (is.numeric(values)){
        values = signif(values, digits=digits)
      }
    }
  }
  
  if (row.names){
    if (col.names){
      write.table(matrix(c(head, colnames(values)), nrow=1), file=file, sep=sep, quote=quote, col.names=FALSE, row.names=FALSE, append=append, na=na)
    }
    write.table(values, file=file, sep=sep, quote=quote, col.names=FALSE, row.names=TRUE, append=TRUE, na=na)
  } else {
    write.table(values, file=file, sep=sep, quote=quote, col.names=col.names, row.names=FALSE, append=append, na=na)
  }
}