search

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
Other
100 stars 67 forks source link

Re-run GSEA module with V22 #1463

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR re-runs the gene_set_enrichment_analysis module with V22. A couple changes had to be made along the way - one of the result tsv files got a bit large (61 MB), and while this won't break git, git doesn't like it and complained. So I updated the code so that all result files are now RDS, and we're back down to 49 MB.

I additionally updated (but did not run!) the relevant figures script to be able to read in this new format.

sjspielman commented 2 years ago

I'll note also that write_rds() does not compress by default (in contrast to saveRDS), so if we are concerned about size, we should probably include compression.

Did not know this about its default! Good to know. I'll update this with .tsv.gz.

sjspielman commented 2 years ago

@jashapiro This has been updated with .gz compression.