[BioC] RE ChIPPEAKANNO

[Zhu, Lihua (Julie)]

Joanne and Dingxia,

You need to call annotatePeakInBatch with your peaks and the Annotation you obtained. By calling data(annotatedPeak), you are running the examples in the ChIPpeakAnno package.

Best regards,

Julie


From: "Ngeow, Joanne" <ngeowj at ccf.org>
Date: Wed, 29 Aug 2012 16:17:21 -0400
To: Lihua Julie Zhu <julie.zhu at umassmed.edu>
Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
Subject: Re: RE ChIPPEAKANNO

Dear Julie,

Thanks. I’ve attached it in the files. The output I got is shown but I would like to identify what the peaks are and I am struggling with that as well as am not sure if I am extracting the info correctly from ensembl for miRNA

Thank you
Joanne


On 8/27/12 6:25 PM, "Zhu, Lihua (Julie)" <Julie.Zhu at umassmed.edu> wrote:

Joanne,

Could you please send us the code snippet and session info? Thanks!

Best regards,

Julie


On 8/27/12 4:00 PM, "Ngeow, Joanne" <ngeowj at ccf.org> wrote:

Hi Julie,
I was using ChIPPeakAnno and was able to extract the distance to nearest miRNA which is what I am interested in. I am having trouble however going from that step to finding out which are the miRNAs that is being mapped.Can’t find the answer online/ blogs.  Can you help?

Thank you

Best regards
Joanne Ngeow
Cancer Genetics Fellow

===================================

Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2012).  Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note:  This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law.  If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited.  If you have received this communication in error,  please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.  Thank you.



===================================

Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2012).  Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note:  This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law.  If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited.  If you have received this communication in error,  please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.  Thank you.


------ End of Forwarded Message