Hi Yuliang,

What is your test.bed look like? It should be a data frame.  If you have a bed file named test.bed, you would first read the test.bed into R as test.bed = read.table(“bedfile.txt”, sep=”\t”, skip=1,header=FALSE) before calling function BED2RangedData.

Could you please type test.bed[1:5,] to see what is the content of the first five rows of the data?

How many rows in test.bed data frame? Please include sessionInfo() in your email.

Please follow the examples by typing ?BED2RangedData in a R console.

Best regards,

Julie


On 9/16/10 6:50 PM, "Yuliang Tan" <yuliangtan@gmail.com> wrote:

Hi Julie,

Thanks for your help! I have another problem when i run BED2RangedData(test.bed,header=TRUE),
It got:
Error in DataFrame(...) : cannot coerce class "numeric" to a DataFrame
R(156,0xa02c9720) malloc: *** mmap(size=105365504) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(156,0xa02c9720) malloc: *** mmap(size=105365504) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(156,0xa02c9720) malloc: *** mmap(size=105365504) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Do you thin it is because of my bed or some packages i doesn't install?

Best,

Yuliang

On Thu, Sep 16, 2010 at 5:54 AM, Zhu, Julie <Julie.Zhu@umassmed.edu> wrote:
Hi Yuliang,

The mouse TSS annotation is TSS.mouse.NCBIM37. You can also get the annotation using the function getAnnotation.

You will find this information if you type in R console,
library(ChIPpeakAnno)
?annotatePeakInBatch
?getAnnotation

For detailed information on how to use the package, please refer to the paper in BMC Bioinformatics (http://www.biomedcentral.com/1471-2105/11/237) and ChIPpeakAnno practical presentation given at Bioc2010 conference (http://www.bioconductor.org/help/course-materials/2010/BioC2010/BioC2010_ChIPpeakAnno.pdf).

Kind regards,

Julie



On 9/15/10 9:42 PM, "Yuliang Tan" <yuliangtan@gmail.com <http://yuliangtan@gmail.com> > wrote:

Hi Zhu:

I'm trying to do some analysis by ChIPpeakAnno, but it seems that there are no mouse genome database in this package, could you tell me how to build an annotation file for this package?  Thank you!



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