Hi Ludwig -- It would be really great to see what you've put together; can you make your code available somewhere, maybe via github?
I think the facilities already in Bioconductor include: - select() and the OrganismDb (e.g., Homo.sapiens) packages - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() - GSEABase mapIdentifiers() - The AnnotationFuncs package (some of this functionality might be redundant with select() / mapIds(); maybe your idea is a more refined version of this? - biomaRt, including the relatively under-known use of select() with mart objects. I think a particularly valuable development (initial implementation in GenomicFeatures::mapIds()) is transparent mapping to / from genomic ranges. The original intention of the annotation() slot in ExpressionSet was to include the microarray chip identifier, so that one references this when translating from probeset to gene identifiers. Martin ________________________________________ From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] Sent: Thursday, December 17, 2015 5:05 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment Dear Bioc Team, I have implemented mapIds methods mapping featureNames (ExpressionSet) and rownames (SummarizedExperiment) between major gene ID types such as ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. Given an ExpressionSet/SummarizedExperiment and an organism under investigation such as 'Homo sapiens', the methods are checking whether the corresponding org.db package is available, otherwise the package is automatically installed and loaded. Subsequently, the featureNames/rownames are mapped from the specified from.id.type to the desired to.id.type, corresponding to keytypes of the org.db package. Options to deal with NA and duplicate mappings are also provided in order to ensure that featureNames/rownames are unique after the mapping. Advantage is that end users do not require knowledge of the Bioc annotation infrastructure, but rather just need to provide the organism under investigation in a convenient format also for non-Biocs. I have not found something similar in existing packages and I am wondering whether this could be something of general interest. Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de _______________________________________________ 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
