Closed hypercompetent closed 6 years ago
Hi Lucas, Thanks for the comments, I’ll take a look. A request: can you make this pull request to our cicero-release repo? This repo is here while I work out bioconductor submission, but all our testing is run on the other one
Will do. Thanks!
Hi Cole and the CICERO team,
Thanks for this great tool! We're using it to dig into our scATAC-seq data from mouse VISp.
This pull has updates to make_cicero_cds() that I think will speed up this step of the process - mostly by keeping things as numeric/matrix as much as possible to reduce type switching.
Below is timing using the original version (make_cicero_cds() ) compared to this version (renamed faster_cicero_cds() ) for my data using chr18.
This passes all of the tests in the "make_cicero_cds aggregates correctly" test section, but I don't know the cds system super well, so I'm not 100% sure this doesn't break anything downstream. If there's something that this breaks, please let me know, and I'll modify and recommit to this branch.
Cheers, -Lucas Graybuck