Deepak, Jianhong has added a function addGeneIDs for adding gene symbol, entrezID...to annotatedPeak or enrichedGO (>=1.9.8). Please let us know how it works out for you. Many thanks for your invaluable feedback! For those of you who attended the ChIPpeakAnno workshop in Bioc2011 meeting last Friday, here is the update per your request (>=1.9.8). 1. Updated documentation for the new function peaksNearBDP (peaks near bi-directional promoter) 2. Updated documentation for annotatePeakInBatch (defaults are specified) 3. makeVennDiagram function now has a new field called useFeature (TRUE/FALSE). TRUE means that the overlapping will be calculated using the feature field in annotatedPeak for deriving overlapping statistics and drawing diagram. FALSE means that the overlapping will be calculated using the chromosome ranges as in the previous versions. The default is FALSE for backward compatibility. Thanks so much for all your invaluable input and positive feedback! Best regards, Julie On 7/29/11 10:36 AM, "Deepak Grover.CTR" <deepak.grover.ctr at="" usuhs.mil=""> wrote: > Thank you for the response, Dr. Zhu. > I will look forward to those updates which bring HUGO sumbols to the table. > > I haven't been able to use the getBM command successfully for mouse gene > symbols. > Can you suggest me what should the syntax be, if you people have already done > it. > > Thanks again, > Deepak > > > > > > Classification: UNCLASSIFIED > Caveats: None >>>> "Zhu, Lihua (Julie)" <julie.zhu at="" umassmed.edu=""> 7/28/2011 4:46 PM >>> > Deepak, > > Jianhong is working on adding gene symbol and other IDs to the annotated > peaks. We will keep you updated. > > Meanwhile, you could use getBM function in biomaRt to get gene symbols. > Thanks! > > Best regards, > > Julie > > > On 7/28/11 9:50 AM, "Deepak Grover.CTR" <deepak.grover.ctr at="" usuhs.mil=""> wrote: > >> Dear Ms. Zhu, >> >> I am a researcher working on mouse chip-seq at USUHS, bethesda. I am trying >> to >> employ your bioconductor package for the annotation. I am getting gene IDs in >> ensembl format using TSS.mouse.NCBIM37, however I am looking to do the same >> to >> get back gene symbols(HUGP/hgnc). Can you suggest if there is a quickfix for >> this. >> I was trying convert bed format data for mouse gene annotation using >> "BED2RangedData" but so far did not succeed as that is giving me duplicate >> row >> name error. >> >> I will really appreciate if you can suggest an easy fix to my problem. >> >> Best, >> >> >> >> Deepak Grover, Ph.D. >> Scientist >> Department of Anatomy, Physiology & Genetics >> Uniformed Services University of the Health Sciences >> Room C-2070 >> 4301 Jones Bridge Rd Bethesda, MD 20814 >> 301-295-3817 >> Deepak.Grover.CTR at usuhs.mil >> http://www.usuhs.mil/ >> >> >> >> >> Classification: UNCLASSIFIED >> Caveats: None >> >> >> >> Classification: UNCLASSIFIED >> >> Caveats: None >> >> >> > > > > > Classification: UNCLASSIFIED > > Caveats: None > > >

Deepak, You could download the most recent version from the repository using svn. svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAn no/ Alternatively, you could download ChIPpeakAnno_1.9.9.tar.gz at http://www.bioconductor.org/packages/2.9/bioc/html/ChIPpeakAnno.html (It will take a couple of days for the version 1.9.9 to appear yet). For documentation please type the following commands in a R session Library(ChIPpeakAnno) browseVignettes("ChIPpeakAnno") Or refer to http://www.bioconductor.org/packages/2.9/bioc/vignettes/ChIPpeakAnno/i nst/do c/ChIPpeakAnno.pdf Best regards, Julie On 8/5/11 11:59 AM, "Deepak Grover.CTR" <deepak.grover.ctr at="" usuhs.mil=""> wrote: > Thank you for the update Dr. Zhu. I am looking forward to work with this. > Can you point me to place where I can access the updated version of your > package and documentation. > > Best, > Deepak > > > > > > Classification: UNCLASSIFIED > Caveats: None >>>> "Zhu, Lihua (Julie)" <julie.zhu at="" umassmed.edu=""> 8/4/2011 10:54 PM >>> > Deepak, > > Jianhong has added a function addGeneIDs for adding gene symbol, > entrezID...to annotatedPeak or enrichedGO (>=1.9.8). Please let us know how > it works out for you. Many thanks for your invaluable feedback! > > For those of you who attended the ChIPpeakAnno workshop in Bioc2011 meeting > last Friday, here is the update per your request (>=1.9.8). > > 1. Updated documentation for the new function peaksNearBDP (peaks near > bi-directional promoter) > 2. Updated documentation for annotatePeakInBatch (defaults are specified) > 3. makeVennDiagram function now has a new field called useFeature > (TRUE/FALSE). TRUE means that the overlapping will be calculated using the > feature field in annotatedPeak for deriving overlapping statistics and > drawing diagram. FALSE means that the overlapping will be calculated using > the chromosome ranges as in the previous versions. The default is FALSE for > backward compatibility. > > Thanks so much for all your invaluable input and positive feedback! > > Best regards, > > Julie > > > On 7/29/11 10:36 AM, "Deepak Grover.CTR" <deepak.grover.ctr at="" usuhs.mil=""> > wrote: > >> Thank you for the response, Dr. Zhu. >> I will look forward to those updates which bring HUGO sumbols to the table. >> >> I haven't been able to use the getBM command successfully for mouse gene >> symbols. >> Can you suggest me what should the syntax be, if you people have already done >> it. >> >> Thanks again, >> Deepak >> >> >> >> >> >> Classification: UNCLASSIFIED >> Caveats: None >>>>> "Zhu, Lihua (Julie)" <julie.zhu at="" umassmed.edu=""> 7/28/2011 4:46 PM >>> >> Deepak, >> >> Jianhong is working on adding gene symbol and other IDs to the annotated >> peaks. We will keep you updated. >> >> Meanwhile, you could use getBM function in biomaRt to get gene symbols. >> Thanks! >> >> Best regards, >> >> Julie >> >> >> On 7/28/11 9:50 AM, "Deepak Grover.CTR" <deepak.grover.ctr at="" usuhs.mil=""> wrote: >> >>> Dear Ms. Zhu, >>> >>> I am a researcher working on mouse chip-seq at USUHS, bethesda. I am trying >>> to >>> employ your bioconductor package for the annotation. I am getting gene IDs >>> in >>> ensembl format using TSS.mouse.NCBIM37, however I am looking to do the same >>> to >>> get back gene symbols(HUGP/hgnc). Can you suggest if there is a quickfix for >>> this. >>> I was trying convert bed format data for mouse gene annotation using >>> "BED2RangedData" but so far did not succeed as that is giving me duplicate >>> row >>> name error. >>> >>> I will really appreciate if you can suggest an easy fix to my problem. >>> >>> Best, >>> >>> >>> >>> Deepak Grover, Ph.D. >>> Scientist >>> Department of Anatomy, Physiology & Genetics >>> Uniformed Services University of the Health Sciences >>> Room C-2070 >>> 4301 Jones Bridge Rd Bethesda, MD 20814 >>> 301-295-3817 >>> Deepak.Grover.CTR at usuhs.mil >>> http://www.usuhs.mil/ >>> >>> >>> >>> >>> Classification: UNCLASSIFIED >>> Caveats: None >>> >>> >>> >>> Classification: UNCLASSIFIED >>> >>> Caveats: None >>> >>> >>> >> >> >> >> >> Classification: UNCLASSIFIED >> >> Caveats: None >> >> >> > > > > > Classification: UNCLASSIFIED > > Caveats: None > > >

Dear Julie, is the addGeneIDs function available in the current library or just in the developer version? thanks Andreia On Fri, Aug 5, 2011 at 3:54 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu>wrote: > Deepak, > > Jianhong has added a function addGeneIDs for adding gene symbol, > entrezID...to annotatedPeak or enrichedGO (>=1.9.8). Please let us know how > it works out for you. Many thanks for your invaluable feedback! > > For those of you who attended the ChIPpeakAnno workshop in Bioc2011 meeting > last Friday, here is the update per your request (>=1.9.8). > > 1. Updated documentation for the new function peaksNearBDP (peaks near > bi-directional promoter) > 2. Updated documentation for annotatePeakInBatch (defaults are specified) > 3. makeVennDiagram function now has a new field called useFeature > (TRUE/FALSE). TRUE means that the overlapping will be calculated using the > feature field in annotatedPeak for deriving overlapping statistics and > drawing diagram. FALSE means that the overlapping will be calculated using > the chromosome ranges as in the previous versions. The default is FALSE for > backward compatibility. > > Thanks so much for all your invaluable input and positive feedback! > > Best regards, > > Julie > > > On 7/29/11 10:36 AM, "Deepak Grover.CTR" <deepak.grover.ctr@usuhs.mil> > wrote: > > > Thank you for the response, Dr. Zhu. > > I will look forward to those updates which bring HUGO sumbols to the > table. > > > > I haven't been able to use the getBM command successfully for mouse gene > > symbols. > > Can you suggest me what should the syntax be, if you people have already > done > > it. > > > > Thanks again, > > Deepak > > > > > > > > > > > > Classification: UNCLASSIFIED > > Caveats: None > >>>> "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> 7/28/2011 4:46 PM >>> > > Deepak, > > > > Jianhong is working on adding gene symbol and other IDs to the annotated > > peaks. We will keep you updated. > > > > Meanwhile, you could use getBM function in biomaRt to get gene symbols. > > Thanks! > > > > Best regards, > > > > Julie > > > > > > On 7/28/11 9:50 AM, "Deepak Grover.CTR" <deepak.grover.ctr@usuhs.mil> > wrote: > > > >> Dear Ms. Zhu, > >> > >> I am a researcher working on mouse chip-seq at USUHS, bethesda. I am > trying > >> to > >> employ your bioconductor package for the annotation. I am getting gene > IDs in > >> ensembl format using TSS.mouse.NCBIM37, however I am looking to do the > same > >> to > >> get back gene symbols(HUGP/hgnc). Can you suggest if there is a quickfix > for > >> this. > >> I was trying convert bed format data for mouse gene annotation using > >> "BED2RangedData" but so far did not succeed as that is giving me > duplicate > >> row > >> name error. > >> > >> I will really appreciate if you can suggest an easy fix to my problem. > >> > >> Best, > >> > >> > >> > >> Deepak Grover, Ph.D. > >> Scientist > >> Department of Anatomy, Physiology & Genetics > >> Uniformed Services University of the Health Sciences > >> Room C-2070 > >> 4301 Jones Bridge Rd Bethesda, MD 20814 > >> 301-295-3817 > >> Deepak.Grover.CTR@usuhs.mil > >> http://www.usuhs.mil/ > >> > >> > >> > >> > >> Classification: UNCLASSIFIED > >> Caveats: None > >> > >> > >> > >> Classification: UNCLASSIFIED > >> > >> Caveats: None > >> > >> > >> > > > > > > > > > > Classification: UNCLASSIFIED > > > > Caveats: None > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- ---------------------------------------------------------------------- ----------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]