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On 8/29/12 11:11 AM, "Dingxia Feng" <email@example.com> wrote:
Thanks very much, Julie. The new code works.
Julie, it's my pleasure to keep the thread in the Bioconductor list to
benefit other people. But I don't know how to do this, can you show me
On Wed, Aug 29, 2012 at 7:22 AM, Zhu, Lihua (Julie)
Please use the following command (skip =1 is added). Please keep the
thread in the Bioconductor list so that others can contribute and/or
MyPeakList = BED2RangedData(read.table("TSpeakList.bed", sep=
On 8/28/12 6:43 PM, "Dingxia Feng" <firstname.lastname@example.org <http:="" email@example.com=""> > wrote:
Thanks for the reply. I tried your code, it didn't work for my file.
The error messages are like this:
> MyPeakList = BED2RangedData(read.table("TSpeakList.bed", sep=
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
line 1 did not have 5 elements
I guess the problem is the format of my .bed. I got this file after
using the mosaic peak caller package. The first lines of this .bed
file are like this:
track name=mosaicsPeaks description="MOSAiCS peaks" useScore=1
I also attached this file here, I hope it can help you understand my
data structure. If you need more information about my file, please let
me know, I'll try my best. Thanks for the help.
On Tue, Aug 28, 2012 at 4:27 PM, Zhu, Lihua (Julie)
<firstname.lastname@example.org <http:="" email@example.com=""> > wrote:
If your peak file is in bed format, you could just use the following
to create RangedData.
MyPeakList = BED2RangedData(read.table("peak.bed", sep=
On 8/28/12 5:13 PM, "Dingxia Feng" <firstname.lastname@example.org <http:="" email@example.com=""> > 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.
> 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
> do more for the converted RangedData to get the peaklist? Or which
> shall I keep or delet? Thanks again.
> Best wishes.
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