Stuart Lee
Stuart Lee
See `aggregateWithDots` in https://github.com/Bioconductor/S4Vectors/blob/master/R/aggregate-methods.R for some ideas of how to do this. The current implementations evals in individual slices rather than over all the groups.
Like `purrr::map_dfr` but for GRanges, essentially a wrapper for bind_ranges(lapply(...)). There could be a parallel backend with BiocParallel too.
Currently, this is done in a kludgy way (and I find it hard to remember what is done) and at the time I wrote didn't really know much about NSE/environments....
Implement on ranges objects. --- Some relevant literature from database theory: [GenAp](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0904-1) a distributed SQL for genomics using spark [review paper on interval joins](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.95.1553&rep=rep1&type=pdf) [book on temporal databases](http://dl.acm.org/citation.cfm?id=2673571&CFID=787271709&CFTOKEN=24661396) - in...
should at least throw a warning here like dplyr does
mainly cause it would be nice to have double dispatch and so other developers could implement them on classes like `RangedSummarisedExperiment` etc
Deferred I/O
To summarise our discussion earlier here's what we're going to implement with regards to I/O (see also #15): - [x] `read_bam` with `paired = TRUE` returns a grouped granges grouped...
There was some general confusion about this during the talk/workshop at Bioc2018. People felt it was not intuitive that the anchoring is dropped after a mutate call and that anchoring...
like the rstudio ones https://www.rstudio.com/resources/cheatsheets/