[BioC] BED15 format for rtracklayer

[rcaloger]

The BED15 format is quite nice to represent alternative splicing events 
data (insertion/skipping), the grey scale of the score from the BED 
format is not ideal. Now, thanks to your implementation of BED15 format 
I  can update  the function for visualization of alternative splicing 
events in oneChannelGUI package.
Many thanks, again!
Raffaele

Michael Lawrence ha scritto:
> I guess we weren't sure if anyone wanted that, so it wasn't implemented. I
> just did though, for version 1.5.10. It's not documented yet, but you can do
> stuff like:
>
> track(session, format = "bed15", expNames = c("samp1", "samp2")) <- myTrack
>
> Where 'myTrack' has columns 'samp1' and 'samp2' containing expression
> values.
>
> Or to output every column, it's just:
>
> track(session, format = "bed15") <- myTrack
>
> If the track was imported from an external Bed15 track, then it's automatic:
> track(session) <- myTrack
>
> Hope this works for you,
> Michael
>
> On Mon, Aug 3, 2009 at 8:13 AM, rcaloger <raffaele.calogero at gmail.com>wrote:
>
>   
>> Hi,
>> since I am interested to visualize microarray data on the UCSC genome
>> browser I would like to know if  there is the possibility to use the BED15
>>  format for microarray data visualization in rtracklayer.
>> Cheers
>> Raffaele
>>
>> --
>>
>> ----------------------------------------
>> Prof. Raffaele A. Calogero
>> Bioinformatics and Genomics Unit
>> Dipartimento di Scienze Cliniche e Biologiche
>> c/o Az. Ospedaliera S. Luigi
>> Regione Gonzole 10, Orbassano
>> 10043 Torino
>> tel.   ++39 0116705417
>> Lab.   ++39 0116705408
>> Fax    ++39 0119038639
>> Mobile ++39 3333827080
>> email: raffaele.calogero at unito.it
>>      raffaele[dot]calogero[at]gmail[dot]com
>> www:   http://www.bioinformatica.unito.it
>> Info: http://publicationslist.org/raffaele.calogero
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>     
>
>   


-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero