matchPWM() questions

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Ugo Borello ▴ 340

@ugo-borello-5753

Last seen 7.3 years ago

France

Dear all, I have this transcription factor PWM: > TFpwm [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] A 52 54 25 133 7 25 5 2 0 90 13 31 C 27 113 167 33 167 37 167 167 167 77 167 52 G 78 0 0 1 1 167 6 3 4 6 21 1 T 10 4 13 2 5 39 2 0 15 3 39 82 As you can see the columns sum to different values: [1] 167 171 205 169 180 268 180 172 186 176 240 166 May I still use this PWM as argument for the Biostring function matchPWM()? May I use matchPWM() with more than one PWMs? Could you suggest me how? Thank you for your help Ugo

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ADD COMMENT • link updated 12.7 years ago by Hervé Pagès 16k • written 12.7 years ago by Ugo Borello ▴ 340

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Hervé Pagès 16k

@herve-pages-1542

Last seen 11 hours ago

Seattle, WA, United States

Hi Ugo, On 03/04/2013 05:48 AM, Ugo Borello wrote: > Dear all, > I have this transcription factor PWM: >> TFpwm > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] > A 52 54 25 133 7 25 5 2 0 90 13 31 > C 27 113 167 33 167 37 167 167 167 77 167 52 > G 78 0 0 1 1 167 6 3 4 6 21 1 > T 10 4 13 2 5 39 2 0 15 3 39 82 > > As you can see the columns sum to different values: > [1] 167 171 205 169 180 268 180 172 186 176 240 166 > > > May I still use this PWM as argument for the Biostring function matchPWM()? Yes that's how a PWM (Position Weight Matrix) is expected to be. Sometimes, you even see negative coefficients in a PWM. My understanding is that there is a difference, at least conceptually, between a Position Weight Matrix (PWM) and a Position Frequency Matrix (PFM). Only in the latter you would expect to see only non-negative coefficients and the columns sum to the same value. Note that the input for matchPWM() must be a PWM, not a PFM. As explained in the man page, the PWM() constructor can transform a PFM into a PWM using the algo described in the Wasserman & Sandelin paper. See ?matchPWM for more info. > > May I use matchPWM() with more than one PWMs? Could you suggest me how? No you can't. You need to loop on your PWMs. Cheers, H. > > Thank you for your help > > Ugo > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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

ADD COMMENT • link 12.7 years ago Hervé Pagès 16k

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Thank you very much. Ugo > From: Hervé Pagès <hpages at="" fhcrc.org=""> > Date: Fri, 08 Mar 2013 13:48:08 -0800 > To: Ugo Borello <ugo.borello at="" inserm.fr=""> > Cc: <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] matchPWM() questions > > Hi Ugo, > > On 03/04/2013 05:48 AM, Ugo Borello wrote: >> Dear all, >> I have this transcription factor PWM: >>> TFpwm >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] >> A 52 54 25 133 7 25 5 2 0 90 13 31 >> C 27 113 167 33 167 37 167 167 167 77 167 52 >> G 78 0 0 1 1 167 6 3 4 6 21 1 >> T 10 4 13 2 5 39 2 0 15 3 39 82 >> >> As you can see the columns sum to different values: >> [1] 167 171 205 169 180 268 180 172 186 176 240 166 >> >> >> May I still use this PWM as argument for the Biostring function matchPWM()? > > Yes that's how a PWM (Position Weight Matrix) is expected to be. > Sometimes, you even see negative coefficients in a PWM. > > My understanding is that there is a difference, at least conceptually, > between a Position Weight Matrix (PWM) and a Position Frequency Matrix > (PFM). Only in the latter you would expect to see only non-negative > coefficients and the columns sum to the same value. > > Note that the input for matchPWM() must be a PWM, not a PFM. > As explained in the man page, the PWM() constructor can transform a > PFM into a PWM using the algo described in the Wasserman & Sandelin > paper. See ?matchPWM for more info. > >> >> May I use matchPWM() with more than one PWMs? Could you suggest me how? > > No you can't. You need to loop on your PWMs. > > Cheers, > H. > >> >> Thank you for your help >> >> Ugo >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > 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

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