Dear Bioconductor mailing list, If I have some CSV data in a file like this : Probe Set ID,Alignment Start,Alignment End,Strand,Gene Symbol 1380054_at,167415761, 167416381,+,Phactr3 1368499_at,167437521,167502083,-,Sycp2 1378270_at,167504376,167504858,+,Ppp1r3d 1373656_at,167505691,167506150,-,Ppp1r3d 1395392_at,167508167,167508749,-,Ppp1r3d ... 1392332_at,170985205,170985581,+,Myt1 1375916_at,171012460,171013368,+,Pcmtd2 1374454_at,171013932,171014583,+,Pcmtd2 1398875_at,171021421,171022475,+,Polr3k ... and I want to make a nice graph showing where each probe set aligns along the region between 167400000 bp and 171000000 bp, where would be a good place to start? I guess I would have to use a lot of low level plotting functions, but I would need to create a blank graph to begin with. what would be cool would be a thick vertical line on the left representing the chromosome and vertical lines to the right showing each probeset's alignment to the chromosome, with each line labeled by the ProbeSetID, gene Symbol and strand. Any help would be greatly appreciated. Richard [[alternative HTML version deleted]]

Have you examined the GenomeGraphs vignette? There is plenty of relevant infrastructure there. You may also be interested in the displays provided by the ADAPT database at Patterson Institute. http://bioinformatics.picr.man.ac.uk/adapt/Welcome.adapt On Sat, May 21, 2011 at 9:18 PM, Richard Student <richard.a.student at="" gmail.com=""> wrote: > Dear Bioconductor mailing list, > > If I have some CSV data in a file like this : > > Probe Set ID,Alignment Start,Alignment End,Strand,Gene Symbol > 1380054_at,167415761, > 167416381,+,Phactr3 > 1368499_at,167437521,167502083,-,Sycp2 > 1378270_at,167504376,167504858,+,Ppp1r3d > 1373656_at,167505691,167506150,-,Ppp1r3d > 1395392_at,167508167,167508749,-,Ppp1r3d > > ... > > 1392332_at,170985205,170985581,+,Myt1 > 1375916_at,171012460,171013368,+,Pcmtd2 > 1374454_at,171013932,171014583,+,Pcmtd2 > 1398875_at,171021421,171022475,+,Polr3k > > ... and I want to make a nice graph showing where each probe set aligns > along the region between 167400000 bp and 171000000 bp, where would be a > good place to start? ?I guess I would have to use a lot of low level > plotting functions, but I would need to create a blank graph to begin with. > what would be cool would be a thick vertical line on the left representing > the chromosome and vertical lines to the right showing each probeset's > alignment to the chromosome, with each line labeled by the ProbeSetID, gene > Symbol and strand. > > Any help would be greatly appreciated. > > Richard > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

You can create pretty rich graphics if you convert this to a BED file and then upload to UCSC. If you prefer to do it programmatically, you can use the rtracklayer package. Sean On Sat, May 21, 2011 at 9:18 PM, Richard Student < richard.a.student@gmail.com> wrote: > Dear Bioconductor mailing list, > > If I have some CSV data in a file like this : > > Probe Set ID,Alignment Start,Alignment End,Strand,Gene Symbol > 1380054_at,167415761, > 167416381,+,Phactr3 > 1368499_at,167437521,167502083,-,Sycp2 > 1378270_at,167504376,167504858,+,Ppp1r3d > 1373656_at,167505691,167506150,-,Ppp1r3d > 1395392_at,167508167,167508749,-,Ppp1r3d > > ... > > 1392332_at,170985205,170985581,+,Myt1 > 1375916_at,171012460,171013368,+,Pcmtd2 > 1374454_at,171013932,171014583,+,Pcmtd2 > 1398875_at,171021421,171022475,+,Polr3k > > ... and I want to make a nice graph showing where each probe set aligns > along the region between 167400000 bp and 171000000 bp, where would be a > good place to start? I guess I would have to use a lot of low level > plotting functions, but I would need to create a blank graph to begin with. > what would be cool would be a thick vertical line on the left representing > the chromosome and vertical lines to the right showing each probeset's > alignment to the chromosome, with each line labeled by the ProbeSetID, gene > Symbol and strand. > > Any help would be greatly appreciated. > > Richard > > [[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 > [[alternative HTML version deleted]]