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stephenturner / annotables

R data package for annotating/converting Gene IDs
http://www.gettinggeneticsdone.blogspot.com/2015/11/annotables-convert-gene-ids.html
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Implement framework for building annotables #6

Closed aaronwolen closed 7 years ago

aaronwolen commented 7 years ago

This PR implements a (really simple) homebrew-inspired framework for building/updating annotables.

The basic idea: each annotable is built from a YAML-based file that lives in data-raw/recipes and provides all of the info necessary for calling getBM(). Plus, the key/value pairs in the attributes block are used to rename the columns.

This would make it easy for others to contribute new recipes or just build custom annotables locally.

Note: build-annotables.r doesn't currently build the transcript-centric tables.

stephenturner commented 7 years ago

this is awesome. will review shortly. one thing i want to do simultaneously is switch around the transcript-gene tables to make them out-of-the-box compatible with tximport tx2gene. Anyhow, will review this shortly. I've never used the yaml pkg before for this kind of thing. Looks useful.

aaronwolen commented 7 years ago

tximport support is a great idea. We could definitely refactor this a bit to move in that direction.

stephenturner commented 7 years ago

@aaronwolen this is awesome. i extended the functionality to write out the tx2gene tables, and actually wrote out the data. now, time to open a bunch more issues