[BioC] How to plot microRNA chromosome location

[Sean Davis]

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.
>
> 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