Reading through the rGADEM man pages, I have yet to figure out how to supply PWMs of my own choosing for rGADEM to match against.  MotifDb provides a method ("query") for extracting a list of matrices by various criteria, for instance:

as.list(query(MotifDb, "MA0079.3"))[[1]]

           1          2          3 4           5         6 7 8         9        10         11
A 0.09812228 0.00000000 0.01133501 0 0.000000000 0.1555988 0 0 0.0000000 0.1206778 0.07465079
C 0.20448821 0.71158690 0.76746050 1 0.991641859 0.0000000 1 1 0.7647126 0.7278452 0.56892604
G 0.48900847 0.07350584 0.00000000 0 0.000000000 0.5294252 0 0 0.0000000 0.0000000 0.08403939
T 0.20838104 0.21490726 0.22120449 0 0.008358141 0.3149760 0 0 0.2352874 0.1514770 0.27238379

It would be very handy to pass such a matrix to the GADEM function, along with the DNAStringSet to match against.  Is this possible?  Sorry if it is there, documented, and I missed it.

 - Paul