[BioC] BED15 format for rtracklayer

[rcaloger]

Thanks for the info related to the RGB feature I completely missed that 
point when I red the BED format help on the UCSC browser.
Could please tell me where I can find the instruction to handle the RGB 
BED feature in rtracklayer?
Cheers
Raffaele
Michael Lawrence ha scritto:
> On Tue, Aug 4, 2009 at 11:16 AM, rcaloger <raffaele.calogero at gmail.com>wrote:
>
>   
>> 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!
>>     
>
>
> You're welcome. But wouldn't using the item RGB feature of BED get around
> the grey scale?
>
>
>   
>> 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
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>>
>>>>         
>>>
>>>       
>> --
>>
>> ----------------------------------------
>> 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
>>
>>
>>     
>
>   


-- 

----------------------------------------
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