[BioC] on PWM in biostrings

[Eloi Mercier]

Hi Shouyong,

You can have a look at the function makePWM from the package MotIV.

Cheers,
Eloi

On 12-08-10 10:51 AM, Hervé Pagès wrote:
> Hi Shouyong,
>
> On 08/10/2012 10:19 AM, Shouyong Peng wrote:
>> Hello
>>
>> I was expecting  PWM(x,type="prob") would be equivalent to
>> censensusMatrix(x, as.prob=TRUE) to give a matrix with colSums to 1.
>> May I know what is formula for this "prob" in PWM?
>
> It uses the algorithm described in this paper:
>
>      Wasserman, WW, Sandelin, A., (2004)
>      Applied bioinformatics for the identification of regulatory
>      elements, Nat Rev Genet.,
>      5(4):276-87.
>
> See PWM() man page for the details.
>
> Cheers,
> H.
>
>>
>> Shouyong
>
>


-- 
Eloi Mercier
Bioinformatics PhD Student, UBC
Paul Pavlidis Lab
2185 East Mall
University of British Columbia
Vancouver BC V6T1Z4