BED15 format for rtracklayer
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rcaloger ▴ 500
@rcaloger-1888
Last seen 7.5 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 • 1.1k views
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@michael-lawrence-2759
Last seen 7.9 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]]
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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
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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]]
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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
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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]]
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