Dingxia,

Great! Thanks for letting me know!

If you do not want to subscribe to the list, you may post the message at
http://www.bioconductor.org/help/mailing-list/mailform/

If you want to receive messages posted by others via the mailing list, you may subscribe to the list at https://stat.ethz.ch/mailman/listinfo/bioconductor.

Thanks!

Best regards,

Julie


On 8/29/12 11:11 AM, "Dingxia Feng" <fengdxia@iastate.edu> 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 how? Thanks.

Best.

On Wed, Aug 29, 2012 at 7:22 AM, Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu> wrote:
Dingxia,

Please use the following command (skip =1 is added). Please keep the thread in the Bioconductor list so that others can contribute and/or benefit.  Thanks!

MyPeakList = BED2RangedData(read.table("TSpeakList.bed", sep= "\t",header=FALSE, skip=1))

Best regards,

Julie


On 8/28/12 6:43 PM, "Dingxia Feng" <fengdxia@iastate.edu <http://fengdxia@iastate.edu> > wrote:

Hi, Lihua,

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= "\t",header=FALSE))
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  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
chrI2380023999 MOSAiCS_peak142
chrI158400 158599MOSAiCS_peak126
chrI223000 223399MOSAiCS_peak289

chrI334600 335399MOSAiCS_peak848.5


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.

Best wishes.

On Tue, Aug 28, 2012 at 4:27 PM, Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu <http://Julie.Zhu@umassmed.edu> > wrote:
Dingxia,

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,

Julie


On 8/28/12 5:13 PM, "Dingxia Feng" <fengdxia@iastate.edu <http://fengdxia@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.






	[[alternative HTML version deleted]]

