Dear Xianyong,

Please see my response below. Thanks!

Best regards,

Julie

On 9/12/12 4:41 PM, "Ma, Xian-Yong" <xian-yong.ma@yale.edu> wrote:

Dear Julie:

I would appreciate your help with the following matter:

1, When I do analysis of my data using the program "ExonPlusUtr" to annotate my data, I have confused the output "IncludeFeature" what is means for this? what's difference between the
inside and IncludeFeature?
    IncludeFeature: the peak range includes the entire feature range. If the feature is an exon, then the peak range includes the entire exon range. So the peak range is larger than the feature range.
    Inside : peak resides inside the feature range, which means that the peak range is shorter than the feature range.

2, If the CHIPpeakAnno package can be used to annotate the Exon and Intron, 5UTR and 3UTR separately?

Yes, you can can. Here are a few examples assuming myPeakList is your peaks as RangedData. For details, please type ?getAnnotation and ?annotatePeakInBatch.

        mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
    Annotation.Exon = getAnnotation(mart, featureType="Exon")
    Annotation.5utr = getAnnotation(mart, featureType= "5utr")
       Annotation.3utr = getAnnotation(mart, featureType= "3utr")

    annotatedPeak.Exon = annotatePeakInBatch(myPeakList, AnnotationData=Annotation.Exon)
    annotatedPeak.5utr = annotatePeakInBatch(myPeakList, AnnotationData=Annotation.5utr)
    annotatedPeak.3utr = annotatePeakInBatch(myPeakList, AnnotationData=Annotation.3utr)

Best Regards,


Xianyong





Begin forwarded message:

Date: May 4, 2012 4:44:03 PM EDT
To: "Zhu, Lihua (Julie)" <Julie.Zhu@umassmed.edu>
Subject: Re: question regarding ChIPPeakAnno use

Dear Julie:

I am very glad to hear from you, Thanks again for your nice help and I will let you know the results!

Have a nice weekend!


Xianyong


On May 4, 2012, at 3:42 PM, Zhu, Lihua (Julie) wrote:

Dear Xianyong,

Thanks for the feedback!

Regarding the error you got, it seems to be a memory issue. Could you please take a look at the post at http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg91461.html? I am ccing the list to get input from the experts in memory setting and management.

Best regards,

Julie


On 5/4/12 3:07 PM, "Ma, Xian-Yong" <xian-yong.ma@yale.edu <x-msg://39/xian-yong.ma@yale.edu> > wrote:

Hi, Dear Dr.Zhu:

I got nice results by using your software, and I am still using this soft ware to analyze other data, now I have the following problem and tried two days, I
can't figured out, would you please help me to solve this problem, I am really appreciate! since the file is bigger than 60 Mb (after compressed), I can't send it
directly.

When I used the CHIPAnno software to analysis my data, as problem always exist as following:


> test1.bed=read.table("/Users/xm5/Downloads/ChIPpeakAnno/data/CHIPJ3.bed", sep="\t", skip=0, header=FALSE)
> CHIPJ3 = BED2RangedData(test1.bed, header=FALSE)
> data(TSS.human.GRCh37)
> annotatedPeak = annotatePeakInBatch(CHIPJ3, AnnotationData=TSS.human.GRCh37)
Error: cannot allocate vector of size 14.4 Mb
R(365,0xa0416540) malloc: *** mmap(size=15118336) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug


I don't know what's reason, and I checked the file using other program, it looks OK, would you please help me to figure out, I appreciate your nice help please see the
attached file that I used for this analysis.






Best wishes,

Xianyong





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