[Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Thu Dec 17 11:05:06 CET 2015

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.


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.Geistlinger at bio.ifi.lmu.de

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