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.

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/do c/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.