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
