User: faustfrankenstein

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Posts by faustfrankenstein

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Answer: A: AnnotationDbi: Select - Join order
... For the sake of completion, one elegant way is to mask the global `select` function (, which is expecting an `OrgDbj`, - see your current available `select` functions via `showMethods("select")`) for your current organism package. In your zzz file add to the utmost layer a class setClass("f ...
written 6 months ago by faustfrankenstein0 • updated 6 months ago by Martin Morgan ♦♦ 23k
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Comment: C: AnnotationDbi: Select - Join order
... I just realized the fix you were referring to is *not* the one of adding an additional ID. I am sorry, didn't get that during my first read. Anyhow, I preferred your approach over messing around with a new ID, for this reason I did spend some time implementing yours. And yup, it happened exactly wh ...
written 6 months ago by faustfrankenstein0
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Comment: C: AnnotationDbi: Select - Join order
... I would not say there is anything wrong with those ideas, for me it's rather a question of efficiency and elegant style. Let's say, I am choosing my annotation package to rely on one huge `data.frame` and assign unique ids, which cannot be transcript ids anymore - that's what I can assure you of. I ...
written 6 months ago by faustfrankenstein0
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Comment: C: AnnotationDbi: Select - Join order
... I was realizing it the moment I hit the 'submit' button. Sometimes, late at night, 'answer', 'respond' and 'reply' appear to be semantically equivalent concepts. Seriously, I beg your pardon for it. The SQLite join is giving me some headaches - I am wondering, whether it might be a more suitable w ...
written 6 months ago by faustfrankenstein0
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Answer: A: AnnotationDbi: Select - Join order
... Uha, I see. First of all, thank you very much for your thoroughly answer. I somehow suspected the underlying SQLite architecture (indeed, I hadn't have a look at it, yet) would only permit such a rather user-unfriendly solution. Thing is, I would like to deploy an organism package and relieve the u ...
written 6 months ago by faustfrankenstein0
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AnnotationDbi: Select - Join order
... Hey everyone, I am working with the AnnotationForge package, but realised a more general issue wrt. to the `select` command. The results seem to be sensitive to the order passed to the `colums` parameter, and do in some cases not contain all the data. Let me give a working example to illustrate ...
annotationdbi written 6 months ago by faustfrankenstein0

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