Re: [Bioc-devel] include .DollarNames.ExpressionSet in Biobase?
Oops, I forgot to mention that I implemented this in devel, version 2.31.1. It's in SVN now and all being well via biocLite() on Saturday afternoon Eastern time. From: Morgan, Martin Sent: Friday, December 04, 2015 9:22 AM To: Philipp Angerer; Bioc-devel Subject: RE: [Bioc-devel] include .DollarNames.ExpressionSet in Biobase? Hi Phillip -- es$foo accesses phenoData(es)$foo, so I implemented .DollarNames.eSet for this. An ExpressionSet is rectangular and has two-dimensional subsettings, the core data is a matrix, and generally ExperessionSet behaves like a matrix. So rather than names() try colnames(). Thanks for the suggestion. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Philipp Angerer [philipp.ange...@helmholtz-muenchen.de] Sent: Friday, December 04, 2015 7:34 AM To: Bioc-devel Subject: [Bioc-devel] include .DollarNames.ExpressionSet in Biobase? Hi, the S3 generic .DollarNames is used to create tab completions in the R command line and RStudio. since you can access featureData(es)$feature via es$feature, it would be useful to either implement .DollarNames.ExpressionSet or simply names.ExpressionSet I couldn’t find a bug tracker for BioConductor, so i posted this here. Best, Philipp Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] include .DollarNames.ExpressionSet in Biobase?
Hi Phillip -- es$foo accesses phenoData(es)$foo, so I implemented .DollarNames.eSet for this. An ExpressionSet is rectangular and has two-dimensional subsettings, the core data is a matrix, and generally ExperessionSet behaves like a matrix. So rather than names() try colnames(). Thanks for the suggestion. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Philipp Angerer [philipp.ange...@helmholtz-muenchen.de] Sent: Friday, December 04, 2015 7:34 AM To: Bioc-devel Subject: [Bioc-devel] include .DollarNames.ExpressionSet in Biobase? Hi, the S3 generic .DollarNames is used to create tab completions in the R command line and RStudio. since you can access featureData(es)$feature via es$feature, it would be useful to either implement .DollarNames.ExpressionSet or simply names.ExpressionSet I couldn’t find a bug tracker for BioConductor, so i posted this here. Best, Philipp Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] include .DollarNames.ExpressionSet in Biobase?
Hi, the S3 generic .DollarNames is used to create tab completions in the R command line and RStudio. since you can access featureData(es)$feature via es$feature, it would be useful to either implement .DollarNames.ExpressionSet or simply names.ExpressionSet I couldn’t find a bug tracker for BioConductor, so i posted this here. Best, Philipp Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
