[BioC] ChIPpeakAnno "examplePattern.fa" file

[Zhu, Lihua (Julie)]

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, "José Luis Lavín" <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, "José Luis Lavín" <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
>>> 
>>> 
>>> 
>>> 
>> 
> 
>