Thank you Bert, I set up a new thread on BioStars [1]. So far, I'm a bit unfamilliar with Bioconductor (but will hopefully attend a course about it in November, which I'm kinda hyped about), other than installing and updating R packages using BiocManager .... Did you think of something else than BioStars.org when saying ?Bioconductor?? The question could be viewed as gene related, but I think it is really about how can one easier than with sqlite handle large tsv files, and why is that parser thing so slow ... I think this is more like a core R thing than gene related question ... [1] https://www.biostars.org/p/9492486/ -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20211006/659983b5/attachment.sig>
https://support.bioconductor.org and the community slack (sign up at https://bioc-community.herokuapp.com/ ) as well as the general site https://bioconductor.org . Actually your question sounds like a SQLite question ? JOIN a table, versus parameterized query. One could perhaps construct the relevant example at the sqlite command line? Martin Morgan On 10/6/21, 2:50 PM, "R-help" <r-help-bounces at r-project.org> wrote: Thank you Bert, I set up a new thread on BioStars [1]. So far, I'm a bit unfamilliar with Bioconductor (but will hopefully attend a course about it in November, which I'm kinda hyped about), other than installing and updating R packages using BiocManager .... Did you think of something else than BioStars.org when saying ?Bioconductor?? The question could be viewed as gene related, but I think it is really about how can one easier than with sqlite handle large tsv files, and why is that parser thing so slow ... I think this is more like a core R thing than gene related question ... [1] https://www.biostars.org/p/9492486/ [[alternative HTML version deleted]]
Since the sqlite package is contributed, it is NOT related to "core R", and is in fact technically off-topic on this list. FWIW all SQL implementations work better with indexes, but AFAIK the R data frame support does nothing with indexes. This may be related to your question, or not. I am not a regular sqlite user. As for fast reading of tsv files, I think arrow, readr, and data.table packages all offer high-performance import functions that could be relevant. On October 6, 2021 11:49:55 AM PDT, Rasmus Liland <jral at posteo.no> wrote:>Thank you Bert, I set up a new thread on >BioStars [1]. So far, I'm a bit >unfamilliar with Bioconductor (but will >hopefully attend a course about it in >November, which I'm kinda hyped about), >other than installing and updating R >packages using BiocManager .... Did you >think of something else than >BioStars.org when saying ?Bioconductor?? > >The question could be viewed as gene >related, but I think it is really about >how can one easier than with sqlite >handle large tsv files, and why is that >parser thing so slow ... I think this >is more like a core R thing than gene >related question ... > >[1] https://www.biostars.org/p/9492486/-- Sent from my phone. Please excuse my brevity.