Jose, Thanks for your kind word! You might want to check out rGADEM package for de nova motif discovery. Best regards, Julie On 2/27/13 11:29 AM, "Jos? Luis Lav?n" <joluito at="" gmail.com=""> wrote: > Thank you Julie, > > I misunderstood the functionality and thought I was a "de novo" motif > finder... > Any insight on how to predict motifs from ChIPseq experiments? Any R module > that does it and you can recommend? May you think of implementing this > function to your awesome package? > ;) > > JL > > 2013/2/27 Zhu, Lihua (Julie) <julie.zhu at="" umassmed.edu=""> >> Jose, >> >> Thanks for the inquiry! I will add the following to the documentation. >> >> The examplePattern.fa, in fasta format, is included in the package as an >> example pattern file for running function summarizePatternInPeaks. To use >> this function, you will need to create your own custom pattern file with the >> pattern(s) you are interested in searching in the peaks. >> >> The pattern file is in fasta file format. The base in the pattern consists >> of IUPAC designated nucleotide symbols such as A, C, G, T, N, V, H, D.... >> >> The bottom table on http://pgfe.umassmed.edu/ZFPsearch.html lists the >> abbreviation codes for degenerate bases. >> >> Best regards, >> >> Julie >> >> >> On 2/27/13 10:54 AM, "Jos? Luis Lav?n" <joluito at="" gmail.com=""> wrote: >> >>> When looking for motif occurrence in the peaks, the "examplePattern.fa" file >>> you supply with the module: >>> >>> -Is a standard example pattern file you can use for any set under analysis >>> or >>> is it a custom one you include in the package referred to a particular set >>> of >>> motifs? >>> >>> -May you give a hint on how to create such kind of file myself? >>> >>> Thanks in advance >>> >>> JL >>> >>> >>> >>> >> > >