Any possibility to "cache" TxDb object?
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aush ▴ 40
@aush-9128
Last seen 12 months ago
United States

In my code, I create a TxDb object from makeTxDbFromEnsembl() call. Every time I run the code, it takes quite a long time - connecting to ensembl server, fetching the data, etc. - even though the data on the server did not change. Is there any way to avoid this by saving the database locally and then only checking that the current database release (i.e. the string like homo_sapiens_core_99_38) is the same?

GenomicFeatures TxDb • 348 views
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@steve-lianoglou-2771
Last seen 2 hours ago
United States

Yes, take a look at the "Saving and Loading a TxDb Object" section of the GenomicFeatures vignette.

There is a pair of saveDb() and loadDb() functions that do exactly what you want.

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Great, thank you Steve!