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
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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
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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