write.table writes unwanted leading empty column to header when has rownames

check this example:

> a = matrix(1:9, nrow = 3, ncol = 3, dimnames = list(LETTERS[1:3], LETTERS[1:3]))
> a
  A B C
A 1 4 7
B 2 5 8
C 3 6 9

the table displays correctly. There are two different ways of writing it to file...

write.csv(a, 'a.csv') which gives as expected:

"","A","B","C"
"A",1,4,7
"B",2,5,8
"C",3,6,9

and write.table(a, 'a.txt') which screws up

"A" "B" "C"
"A" 1 4 7
"B" 2 5 8
"C" 3 6 9

indeed, an empty tab is missing.... which is a pain in the butt for downstream things. Is this a bug or a feature? Is there a workaround? (other than write.table(cbind(rownames(a), a), 'a.txt', row.names=FALSE)

Cheers, yannick

Solution 1:

Citing ?write.table, section CSV files:

By default there is no column name for a column of row names. If col.names = NA and row.names = TRUE a blank column name is added, which is the convention used for CSV files to be read by spreadsheets.

So you must do

write.table(a, 'a.txt', col.names=NA)

and you get

"" "A" "B" "C"
"A" 1 4 7
"B" 2 5 8
"C" 3 6 9

Solution 2:

A slight modification to @Marek very helpful answer WILL add a header to the rownames column: temporarily add the rownames as the first column in the data.frame, and write that, ignoring the real rownames.

> a = matrix(1:9, nrow = 3, ncol = 3, dimnames = list(LETTERS[1:3], LETTERS[1:3]))
> write.table(data.frame("H"=rownames(a),a),"a.txt", row.names=FALSE)

and you get

"H" "A" "B" "C"
"A" 1 4 7
"B" 2 5 8
"C" 3 6 9