[Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment

Dear Martin,

I finally found the time to make the code available via GitHub:

https://github.com/lgeistlinger/MapIds

and added you as a collaborator.
This is currently just a quick put-together for you to get an impression.
NA and duplicated mappings currently need to be removed to ensure
uniqueness of featureNames and rownames, respectively (via na.rm=TRUE and
dupl.rm=TRUE).

But there are, of course, other/better ways to summarize over
NA's/Duplicates, e.g. by appropriately passing that on to the 'multiVals'
Argument of AnnotationDbi::mapIds().

Just let me know in case you find that of any use or you find things that
could be improved/extended.

Best,
Ludwig



---

Dear Martin,

Ok, I am tyding that up and provide that via GitHub for you.
BTW, these ranges to Ids and vice versa sounds very cool!


> 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.

One question to that, as I often find my functions to ask for the organism
uder study (which I believe is actually most typically known when
investigating an expression dataset). While there are convenient ways to
ask microarray annotation packages for the organism under study (and thus
infer it from annotation(eset)), I wonder whether there is a similar slot
for SummarizedExperiment, eg an 'organism' slot? Or are there specific
reasons arguing against that?

Best,
Ludwig


> 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... at r-project.org] on behalf of Ludwig
> Geistlinger [ludwig.geistlin... at bio.ifi.lmu.de]
> Sent: Thursday, December 17, 2015 5:05 AM
> To: bioc-devel at 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 f?r Bioinformatik
> Institut f?r Informatik
> Ludwig-Maximilians-Universit?t M?nchen
> Amalienstrasse 17, 2. Stock, B?ro A201
> 80333 M?nchen
>
> Tel.: 089-2180-4067
> eMail: ludwig.geistlin... at bio.ifi.lmu.de
>
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