[BioC] on PWM in biostrings

Hervé Pagès hpages at fhcrc.org
Fri Aug 10 19:51:48 CEST 2012

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.,

See PWM() man page for the details.


> Shouyong

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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