Consistent use of text output formats - csv, tsv

There are varying output formats across the package - ```write.table('*.txt', sep = ",")```, ```write.table('*.txt', sep = "\t")```, ```write.csv('*.csv')```, ```write.csv('*.txt')```

We should decided on the preferred output and/or just be explicit when outputting - comma-delimited = `.csv`,  tab-delimited  =`.txt` ..i.e. should not have `write.table` to a `.txt` with a `sep=","` 