BED15 format for rtracklayer
1
0
Entering edit mode
rcaloger ▴ 500
@rcaloger-1888
Last seen 9.1 years ago
European Union
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
Microarray Visualization rtracklayer Microarray Visualization rtracklayer • 1.6k views
ADD COMMENT
0
Entering edit mode
@michael-lawrence-2759
Last seen 9.6 years ago
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@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@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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode
On Tue, Aug 4, 2009 at 11:16 AM, rcaloger <raffaele.calogero@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@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@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@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@unito.it > raffaele[dot]calogero[at]gmail[dot]com > www: http://www.bioinformatica.unito.it > Info: http://publicationslist.org/raffaele.calogero > > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
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 >>>> >>>> _______________________________________________ >>>> 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 >> >> >> > > -- ---------------------------------------- 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
ADD REPLY
0
Entering edit mode
Just put "color" as a column in the RangedData. It can be in any format accepted by col2rgb(). Michael On Wed, Aug 5, 2009 at 7:08 AM, rcaloger <raffaele.calogero@gmail.com>wrote: > 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@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@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@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@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@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@unito.it > raffaele[dot]calogero[at]gmail[dot]com > www: http://www.bioinformatica.unito.it > Info: http://publicationslist.org/raffaele.calogero > > [[alternative HTML version deleted]]
ADD REPLY

Login before adding your answer.

Traffic: 771 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6