[BioC] matchPWM() questions

[Ugo Borello]

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
>> 
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> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
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