[BioC] Conversion of pfm to pwm using PWM()

[Ravi Karra]

Hi, 
I am trying to find TF binding sites in a set of promoters using position frequency matrices (pfm's) from jaspar and transfac.  I have gotten this to work before on my machine at home, but cannot seem to get this to run on campus.  I am not sure why I get the following error as I thought PWM can handle integer pfm's.  Any thoughts?

Thanks in advance, 
Ravi

Code: 
> library (Biostrings)
> pfm
  [,1] [,2] [,3] [,4] [,5] [,6]
A   13    0   50    1   13    6
C   14    0    2    0    6   16
G   15   53    0    1   25   22
T   11    0    1   51    9    9
> typeof (pfm)
[1] "integer"
> pwm = pfm (PWM)
Error: could not find function "pfm"
> library (Biostrings)
> pfm
  [,1] [,2] [,3] [,4] [,5] [,6]
A   13    0   50    1   13    6
C   14    0    2    0    6   16
G   15   53    0    1   25   22
T   11    0    1   51    9    9
> typeof (pfm)
[1] "integer"
> PWM (pfm)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "PWM", for signature "matrix"
> sessionInfo ()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] doMC_1.2.1        multicore_0.1-5   foreach_1.3.0     codetools_0.2-2  
[5] iterators_1.0.3   Biostrings_2.18.4 IRanges_1.8.9     biomaRt_2.6.0    

loaded via a namespace (and not attached):
[1] Biobase_2.10.0 RCurl_1.5-0    tools_2.12.0   XML_3.4-0