On Tue, Aug 4, 2009 at 12:58 AM, Patrick Aboyoun <[email protected]> wrote:
> Purna, > Are you looking to visualize the letters or the locations? If its the > locations your after, you might want to look to see what rtracklayer (genome > browser integration), GenomeGraphs (plots genomic information from Ensembl) > and HilbertVis (maps 1d vector into 2d space for better understanding of > spatial relationships) have to offer. Their respective vignettes are at > > > http://bioconductor.org/packages/2.5/bioc/vignettes/rtracklayer/inst/doc/rtracklayer.pdf For rtracklayer, the simplest way is: browseGenome(GenomicData(mychr, genome = "hg18")) That assumes your reference genome is hg18. > > http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf > > http://bioconductor.org/packages/2.5/bioc/vignettes/HilbertVis/inst/doc/HilbertVis.pdf > > You may need help getting your data into a form to feed into a graph that > interests you. If so, make sure you provide specifics like your R > sessionInfo(), the reference genome you are using, and any other information > that can help others help you. > > > Patrick > > > > Purnachander wrote: > >> Dear all, >> >> I've loaded a complete genome into variable "mychr" and created many views >> of it. >> How can I represent all the generated views in a graphical plot? >> >> " mychr" is : >> 1860725-letter "DNAString" instance >> seq: >> TGGTACCGGAAGCTATGCGTTAAAAAAGGAATAATG...GCAATTACCGGTAACGAAAAATTTCATGCGCCTTTC >> >> Views generated are : >> views: >> start end width >> [1] 2231 11434 9204 >> [GAGGTATGGAAACCTGATCTAGCC...TTCACCATAGTCGATTATAACAC] >> [2] 11784 18426 6643 >> [GTCACATCCGGGATTTTGCTCTGG...CCTTTTCTTCGTTGAGAAATTTC] >> ... ... ... ... ... >> [366] 1851121 1856489 5369 >> [GAAGTGGTAACCTCTGATCCTTCA...CATCATCATGAAGTCGAACGGAT] >> [367] 1858686 1860020 1335 >> [TTCAAATGTTCGTAATACTTTTCA...ACGAATCTTGCCAACCTCATAGT] >> >> How can I graphically represent these views on a reference genome? >> >> Regards, >> Purna >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
