Hi Eloi & Herve, Thank you both for your help. Shouyong On Fri, Aug 10, 2012 at 2:18 PM, Eloi Mercier 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 > > [[alternative HTML version deleted]]