[BioC] matchPWM() questions
Hervé Pagès
hpages at fhcrc.org
Fri Mar 8 22:48:08 CET 2013
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
Fred Hutchinson Cancer Research Center
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