Hi,

I used str() on my data set:

$ X1            : num  1 1 0 1 1 1 1 1 1 1 ...
$ X2            : num  0 1 0 2 1 2 0 2 2 0 ...
$ X3            : Factor w/ 4 levels "0","1","2","NA": 2 1 3 1 1 1 1 1 1 3
...
....


The difference to your str() output is that in your case NA columns are
"num" columns
and in my case they are Factors. That's prob. why it replaces the NAs with 4
after
applying data.matrix.

I use the package xlsx to read the data in as an excel file.

Cheers
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