Consistent use of text output formats - csv, tsv

[Shaunson26]

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=","