[BioC] PWMEnrich binding site position

[Robert Stojnic]

Hi Massimo,

Once you have identified enriched motifs you can use the function 
motifScores() to find their raw motifs score along a sequence. The 
latest version of the package (currently in development) explains how to 
do this in the vignette:

http://bioconductor.org/packages/2.13/bioc/vignettes/PWMEnrich/inst/doc/PWMEnrich.pdf

Some of the plotting functions will not be available in the your version 
of PWMEnrich, but the motifScores() function works the same. The only 
important thing to know about this function is that it returns the PWM 
scores in real (and not log) space. Therefore, to apply a conventional 
score cutoff of 4 or 5 you will need to take the log of raw scores 
returned by this function.

Cheers, r.


On 06/09/13 08:43, massimo acquaviva [guest] wrote:
> Hallo to everyone,
> I'm using PWMEnrich to search for enriched TFBS in a list of FASTA sequences.
> I can't understand how to extract the coordinates of the matches for the enriched motifs,
>
> Any suggestion will be highly appreciated
>
> Thank you in advance
>
> Massimo Acquaviva
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
> [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
> [5] LC_TIME=Italian_Italy.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
> Sent via the guest posting facility at bioconductor.org.