[BioC] How to plot microRNA chromosome location

[Camper (Chih-Wei Liu)]

Thank you very much.
This package is very useful too.
However, if I want to plot all miRNAs in one chromosome, it doesn't work.

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Michael
Lawrence
Sent: Saturday, November 01, 2008 9:27 AM
To: Sean Davis
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] How to plot microRNA chromosome location

On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:

> On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
> > Hi,
> >
> > On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote:
> >
> >> Hi all,
> >>
> >>
> >>
> >> I have check some useful packages to plot gene chromosome information
> like
> >> gene plotter, ideogram and GenomeGraphs.
> >>
> >> However, I don't know how to plot microRNA (miRNA) chromosome location.
> >>
> >> I would like to see the distribution of some miRNAs in the genome.
> >>
> >>
> >>
> >> I have known the miRNA chromosome info.
> >>
> >> miRNA name           chromosome           start           end
> >>
> >> hsa-miR-130b            22                             20337592
> >> 20337673
> >>
> >> hsa-miR-33a              22                             40626894
> >> 40626962
> >>
> >> hsa-miR-15b              3                              161605069
> >> 161605166
> >>
> >> .
> >>
> >>
> >>
> >> Is there any packages that I provide the location and plotting it out?
> >
> > You could create a custom track and upload it to the UCSC genome
browser.
> >
>


Sorry for late reply here. In fact, there is an example in the rtracklayer
vignette that does pretty much exactly this, except with miRNA target sites.

Let me know if you need any more guidance.

Thanks,
Michael


> > It looks like you got your info about 90% the way to GFF format:
> >
> > http://genome.ucsc.edu/FAQ/FAQformat#format3
> >
> > You could tweak your info a bit, then write.table your way to a file you
> can
> > upload as a UCSC custom track.
>
> See the rtracklayer package for help here.
>
> > Is that good enough, or were you looking for something more? And if so,
> > what? There's the GenomeGraphs library, which is pretty slick, but I'm
> not
> > sure if that's really what you're after:
> >
> > http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html
>
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