[BioC] on PWM in biostrings
emercier at chibi.ubc.ca
Fri Aug 10 20:18:14 CEST 2012
You can have a look at the function makePWM from the package MotIV.
On 12-08-10 10:51 AM, Hervé Pagès wrote:
> Hi Shouyong,
> On 08/10/2012 10:19 AM, Shouyong Peng wrote:
>> 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.,
> See PWM() man page for the details.
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