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@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. [[alternative HTML version deleted]]

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.

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@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

Joanne, Given a peak dataset peaks in RangedData and an annotation dataset miRNAs you obtained from getAnnotation, then you can use the following code to obtain the nearest miRNAs. nearest.miRNAs = as.data.frame(annotatePeakInBatch(peaks, AnnotationData = miRNAs)) Please type ?annotatePeakInBatch in R to view other examples. You can also access the documentation at http://www.bioconductor.org/p ackages/2.10/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf, and the publication at http://www.biomedcentral.com/1471-2105/11/237/. Best regards, Julie On 8/30/12 4:02 PM, "Ngeow, Joanne" <ngeowj@ccf.org> wrote: Dear Julie, Thank your for your response but I am unclear as to what you mean by that- do you have a sample of the code to use to 1. get ensembl data for miRNA 2. correlate with my peaks 3. identify which miRNAs are the ones called out I am sorry but I am very new to ChIPpeakAnno as you can tell. For TSS, it is easier to find solutions on line but I can’t seem to find what I need on miRNAs Thank you, your help is much appreciated Joanne On 8/29/12 6:04 PM, "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> wrote: 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@ccf.org> Date: Wed, 29 Aug 2012 16:17:21 -0400 To: Lihua Julie Zhu <julie.zhu@umassmed.edu> Cc: "bioconductor@r-project.org" <bioconductor@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@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@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 =================================== 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. [[alternative HTML version deleted]]