[BioC] ChIPpeakAnno

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Tue Aug 28 23:27:49 CEST 2012


If your peak file is in bed format, you could just use the following command
to create RangedData.

MyPeakList = BED2RangedData(read.table("peak.bed", sep= "\t",header=FALSE))

Best regards,


On 8/28/12 5:13 PM, "Dingxia Feng" <fengdxia at iastate.edu> wrote:

> Hello, Lihua,
> I'm interested in your ChIPpeakAnno package, but I'm a pure biologist not good
> at R stuff. My peak file is peak.bed. I want use what you mentioned
> RfunctionGFF2RangedData to convert it to RangedData, but I don't know how to
> do this, I mean I don't know what shall I type after the R prompt. Would you
> please do me a favor to show me the code for this? Thanks.
> And I found in your example code, you use data (myPeakList), so do I need to
> do more for the converted RangedData to get the peaklist? Or which columns
> shall I keep or delet? Thanks again.
> Best wishes.

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