Dear All, Thank you kindly for such detailed replies. I was looking to overlay data using algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz since it wouldn't work on R 2.14, would try it after upgrading to R 2.15. Other package - ggbio , work on an input 'Object'. I am not able to figure out what to provide as object - gene expression data matrix as whole and or SNP log2 normalised ratios? Any more help or thoguhts here will be greatly appreciated. Thanks a ton ! -E From: Tengfei Yin [mailto:yintengfei@gmail.com] Sent: 23 April 2012 21:30 To: Ekta Jain Cc: bioconductor@r-project.org; r-help@r-project.org Subject: Re: [BioC] Overlay Gene Expression on SNP (copy number) data On Mon, Apr 23, 2012 at 6:33 AM, Ekta Jain <ekta_jain@jubilantbiosys.com<mailto:ekta_jain@jubilantbiosys.com>> wrote: Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Hi Ekta, If you mean visually, as Steve suggested, you could try packages like ggbio, Gviz, Rcytoscape.. it depends on how you plan to visualize your data, track-based? circular view? net work? and what format your data are? for example, in ggbio, it depends on what data you are using, you can arrange your data into GRanges manually or just provide data that rtracklayer supported like bed, then just use autoplot, it accepts different objects, like GRanges, IRanges, bamfiles or character... allow some transformation like coverage. For files like bed, it automatically use bar to represent your data and use score as y(you can specify other y). Function tracks() allow you to bind or overlay any graphics produced by ggbio or ggplot2, so you could work from data.frame too, it will help you align your plots after the graphics are produced. For genomic structure, if you want to overlay with your data, try autoplot, TranscriptDb. And if you want to show interaction between genes, you could try either arches in linear view or links in circular view(layout_circle). http://tengfei.github.com/ggbio/ this website is still under development, just to show some possible cases, it will be re-built against R 2.15 and more case studies are coming. HTH Tengfei Another possibility for visual display of several kinds of data is RCytoscape, for which an example can be seen here: http://rcytoscape.systemsbiology.net/versions/current/gallery/TCGA/sub net.TCGA.02.0014.png This portrays 1) gene expression (green: under-expression; red: over-expression) 2) copy number (blue: high, black: low) 3) gene type (node shape: hexagons are kinases, arrows are ligands, diamonds are receptors, circles for everything else) 4) mutation status (not SNPs, but non-synonymous amino acid substitutions) 5) in the context of gene relationships, from KEGG A vignette for a larger version of this network is nearly complete. The Cytoscape network map is created from data and R code. - Paul Hi, On Mon, Apr 23, 2012 at 7:33 AM, Ekta Jain <ekta_jain@jubilantbiosys.com<mailto:ekta_jain@jubilantbiosys.com>> wrote: > Hello, > Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? I guess you mean visually? If so, I'd suggest skimming through the vignettes of the following packages to see which one might suit you best: * Gviz * ggbio * GenomeGraphs -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact Thanks, Ekta Senior Research Associate Bioinformatics Department Jubilant Biosys Pvt Ltd, #96, Industrial Suburb, 2nd Stage Yeshwantpur, Bangalore 560 022 Ph No : +91-80-66628346<tel:%2b91-80-66628346> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com<http: www.jubl.com=""> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name<http: www.tengfei.name=""> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. 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Have you considered the plots that the 'pint' package generates? Those work under 2.14. You should also upgrade R, mind you. But 'pint' may be to your liking. On Tue, Apr 24, 2012 at 9:15 PM, Ekta Jain <ekta_jain@jubilantbiosys.com>wrote: > Dear All, > Thank you kindly for such detailed replies. I was looking to overlay data > using algorithms so that i am able to tell which genes are differentially > expressed due to changes in copy number. I did a pubmed search and found > only 7 literature pieces all of which use in-house algorithms. I am yet to > explore Gviz since it wouldn't work on R 2.14, would try it after upgrading > to R 2.15. Other package - ggbio , work on an input 'Object'. I am not able > to figure out what to provide as object - gene expression data matrix as > whole and or SNP log2 normalised ratios? > > Any more help or thoguhts here will be greatly appreciated. > > Thanks a ton ! > -E > > From: Tengfei Yin [mailto:yintengfei@gmail.com] > Sent: 23 April 2012 21:30 > To: Ekta Jain > Cc: bioconductor@r-project.org; r-help@r-project.org > Subject: Re: [BioC] Overlay Gene Expression on SNP (copy number) data > > > On Mon, Apr 23, 2012 at 6:33 AM, Ekta Jain <ekta_jain@jubilantbiosys.com> <mailto:ekta_jain@jubilantbiosys.com>> wrote: > Hello, > Can anyone please suggest any packages in R that can be used to overlay > gene expression data on SNP (affymetrix) copy number ? > Hi Ekta, > > If you mean visually, as Steve suggested, you could try packages like > ggbio, Gviz, Rcytoscape.. it depends on how you plan to visualize your > data, track-based? circular view? net work? and what format your data are? > > for example, in ggbio, it depends on what data you are using, you can > arrange your data into GRanges manually or just provide data that > rtracklayer supported like bed, then just use autoplot, it accepts > different objects, like GRanges, IRanges, bamfiles or character... allow > some transformation like coverage. For files like bed, it automatically use > bar to represent your data and use score as y(you can specify other y). > Function tracks() allow you to bind or overlay any graphics produced by > ggbio or ggplot2, so you could work from data.frame too, it will help you > align your plots after the graphics are produced. For genomic structure, if > you want to overlay with your data, try autoplot, TranscriptDb. And if you > want to show interaction between genes, you could try either arches in > linear view or links in circular view(layout_circle). > > http://tengfei.github.com/ggbio/ > > this website is still under development, just to show some possible cases, > it will be re-built against R 2.15 and more case studies are coming. > > HTH > > Tengfei > > > Another possibility for visual display of several kinds of data is > RCytoscape, for which an example can be seen here: > > > > > http://rcytoscape.systemsbiology.net/versions/current/gallery/TCGA/s ubnet.TCGA.02.0014.png > > > > This portrays > > 1) gene expression (green: under-expression; red: over-expression) > > 2) copy number (blue: high, black: low) > > 3) gene type (node shape: hexagons are kinases, arrows are ligands, > diamonds are receptors, circles for everything else) > > 4) mutation status (not SNPs, but non-synonymous amino acid substitutions) > > 5) in the context of gene relationships, from KEGG > > > > A vignette for a larger version of this network is nearly complete. The > Cytoscape network map is created from data and R code. > > > > - Paul > > Hi, > > > > On Mon, Apr 23, 2012 at 7:33 AM, Ekta Jain <ekta_jain@jubilantbiosys.com> <mailto:ekta_jain@jubilantbiosys.com>> wrote: > > > Hello, > > > Can anyone please suggest any packages in R that can be used to overlay > gene expression data on SNP (affymetrix) copy number ? > > > > I guess you mean visually? If so, I'd suggest skimming through the > vignettes of the following packages to see which one might suit you > > best: > > > > * Gviz > > * ggbio > > * GenomeGraphs > > > > -steve > > > > -- > > Steve Lianoglou > > Graduate Student: Computational Systems Biology > > | Memorial Sloan-Kettering Cancer Center > > | Weill Medical College of Cornell University Contact Info: > http://cbio.mskcc.org/~lianos/contact > > > Thanks, > Ekta > Senior Research Associate > Bioinformatics Department > Jubilant Biosys Pvt Ltd, > #96, Industrial Suburb, 2nd Stage > Yeshwantpur, Bangalore 560 022 > Ph No : +91-80-66628346<tel:%2b91-80-66628346> > > The information contained in this electronic message and in any > attachments to this message is confidential, legally privileged and > intended only for use by the person or entity to which this electronic > message is addressed. If you are not the intended recipient, and have > received this message in error, please notify the sender and system manager > by return email and delete the message and its attachments and also you are > hereby notified that any distribution, copying, review, retransmission, > dissemination or other use of this electronic transmission or the > information contained in it is strictly prohibited. Please note that any > views or opinions presented in this email are solely those of the author > and may not represent those of the Company or bind the Company. Any > commitments made over e-mail are not financially binding on the company > unless accompanied or followed by a valid purchase order. This message has > been scanned for viruses and dangerous content by Mail Scanner, a! > nd is believed to be clean. The Company accepts no liability for any > damage caused by any virus transmitted by this email. > www.jubl.com<http: www.jubl.com=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Tengfei Yin > MCDB PhD student > 1620 Howe Hall, 2274, > Iowa State University > Ames, IA,50011-2274 > Homepage: www.tengfei.name<http: www.tengfei.name=""> > > > The information contained in this electronic message and in any > attachments to this message is confidential, legally privileged and > intended only for use by the person or entity to which this electronic > message is addressed. If you are not the intended recipient, and have > received this message in error, please notify the sender and system manager > by return email and delete the message and its attachments and also you are > hereby notified that any distribution, copying, review, retransmission, > dissemination or other use of this electronic transmission or the > information contained in it is strictly prohibited. Please note that any > views or opinions presented in this email are solely those of the author > and may not represent those of the Company or bind the Company. Any > commitments made over e-mail are not financially binding on the company > unless accompanied or followed by a valid purchase order. This message has > been scanned for viruses and dangerous content by Mail Scanner, a! > nd is believed to be clean. The Company accepts no liability for any > damage caused by any virus transmitted by this email. > www.jubl.com > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]