Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? 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 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, and 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]]

Hi, On Mon, Apr 23, 2012 at 7:33 AM, Ekta Jain <ekta_jain at="" 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

On Mon, Apr 23, 2012 at 6:33 AM, Ekta Jain <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 > > 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 > > 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 > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]