[BioC] About ChIPpeakAnno

[Zhu, Lihua (Julie)]

Lucia,

If you type help(annotatePeakInBatch), you will see that there is a
parameter "output" with three options. By default, it is set to nearestStart
which will generate nearest features without any distance constraint. If you
set "output" to one of the other two options, then the distance cutoff can
be set by specifying "maxgap", e.g., 5000 as 5kb. Please let me know if this
answers your questions.

Best regards,

Julie


On 3/7/14 2:18 PM, "Lucia Peixoto" <luciap at iscb.org> wrote:

> Hi,
> This is my first time using the package, so maybe this is a naive question
> What is the distance cutoff used to find "nearest feature (gene, exon,
> miRNA,etc)"
> or there isn't any and I can filter on it after the mapping?
> thanks