[BioC] Creating a figure showing Affy probe-set alignments along a small segment of chromosome

[Vincent Carey]

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]]
>
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