[BioC] using cosmo to find multiple DNA motifs

[Paul Shannon]

Dear Oliver,

I am exploring cosmo (v 1.22.0 with R 2.15).  I am happy to see cosmo finding a motif which is shared across the promoters of some genes with correlated expression.  

I use all of the default arguments when invoking cosmo, and I am passing in a list of 45 promoter regions, each 1100 bases long.  I will use longer sequences after I understand cosmo a little better.

I was surprised that just one PWM is found among the 45 sequences:

> motifs at pwm 
       1      2 3      4 5      6      7
A 0.0914 0.4863 0 0.0000 0 0.0000 0.4231
C 0.5009 0.0000 0 0.5808 0 0.3180 0.0000
G 0.4076 0.0586 0 0.0000 1 0.1123 0.0000
T 0.0000 0.4551 1 0.4192 0 0.5697 0.5769

I am stuck at this point:  I don't see how to invoke cosmo so that it will find the other shared motifs which I believe can be found among these promoters.

I read the man pages and studied the vignette, but came away no wiser.

Could you point me in the right direction, please?

Thanks!

 - Paul