Hi Eloi & Herve,

Thank you both for your help.

Shouyong

On Fri, Aug 10, 2012 at 2:18 PM, Eloi Mercier <emercier@chibi.ubc.ca> wrote:

> 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
>
>

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