[BioC] ChIPpeakAnno "examplePattern.fa" file

[Zhu, Lihua (Julie)]

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
> 
> 
> 
>