R help - Jun 2009 - read.table, row.names arg

Dear R users,
I had somehow expected that read.table() would treat the column specified by
the row.names argument as of class character. That seems to be the only
sensible class allowed for a column containing row names. However, that does
not seem to be the case, as the following example shows:

  x <- cbind.data.frame(ID = c("010007787048271871",
"1007109516820319",
"10094843652996959", "010145176274075487"), X1 = 1:4, X2 =
4:1);
    write.table(x, "tmp.txt", quote = FALSE, row.names = FALSE);
    y <- read.table("tmp.txt", header= TRUE, row.names=1)
> y
                  X1 X2
10007787048271872  1  4
1007109516820319   2  3
10094843652996960  3  2
10145176274075488  4  1
> x
                  ID X1 X2
1 010007787048271871  1  4
2   1007109516820319  2  3
3  10094843652996959  3  2
4 010145176274075487  4  1

The first column was not read in as a string, which mangled the IDs.
I could use colClasses explicitly, but then I would need to know the number
and classes of the remaining columns in advance.
Is this a bug or expected behavior ?
Any advice would be most helpful.

Thanks,

Markus

	[[alternative HTML version deleted]]

Markus Loecher <markus.loecher <at> gmail.com> writes:
> [...]
> > x
>                   ID X1 X2
> 1 010007787048271871  1  4
> 2   1007109516820319  2  3
> 3  10094843652996959  3  2
> 4 010145176274075487  4  1
> 
> The first column was not read in as a string, which mangled the IDs.
> I could use colClasses explicitly, but then I would need to know the number
> and classes of the remaining columns in advance.
> Is this a bug or expected behavior ?
> Any advice would be most helpful.
You could use a generic colClasses for all columns, like:

y <- read.table("tmp.txt", header= TRUE, row.names=1,
colClasses="character")
y
                   X1 X2
010007787048271871  1  4
1007109516820319    2  3
10094843652996959   3  2
010145176274075487  4  1

In this case, all columns are read as character and need to be converted
manually, but your row names are appropriate.

Hoping this helps,
Adrian

Markus Loecher-4 wrote:
> 
> Dear R users,
> I had somehow expected that read.table() would treat the column specified
> by
> the row.names argument as of class character. That seems to be the only
> sensible class allowed for a column containing row names. However, that
> does
> not seem to be the case, as the following example shows:
> 
>   x <- cbind.data.frame(ID = c("010007787048271871",
"1007109516820319",
> "10094843652996959", "010145176274075487"), X1 = 1:4,
X2 = 4:1)
> [...snip...]
> 
As a better alternative, why not move directly the first column in the
rownames?

rownames(x) <- x$ID
write.table(x[, -1], "tmp.txt")
y <- read.table("tmp.txt", header=T)
y
                   X1 X2
010007787048271871  1  4
1007109516820319    2  3
10094843652996959   3  2
010145176274075487  4  1

In this case, X1 and X2 variables are read as numeric, while the first
column is read as character and assigned directly to the rownames.

HTH,
Adrian
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