[BioC] matchPWM() questions

[Hervé Pagès]

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

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