search

ncborcherding / escape

Easy single cell analysis platform for enrichment
https://www.borch.dev/uploads/screpertoire/articles/running_escape
MIT License
141 stars 20 forks source link

Improve computational time for EnrichIt(), performPCA(), and masterPCAplot #55

Closed monikaramos closed 2 years ago

monikaramos commented 2 years ago

Hi there! Great package, I am a huge fan!

I am wondering if there is a way to improve the computational time it takes to run the functions performPCA(), and masterPCAplot when considering larger gene sets such as MsigDB's curated gene set C2 that has ~6000+ gene sets to do GSEA on. For example, it took 8 hours to finish running just performPCA(). Is there an ability to specify or increase the multi-core processors or threads?

Thanks!

ncborcherding commented 2 years ago

Hey Monikaramos,

There are several faster PCA options, see here or here. There are also packages for PCA in the context of large data - see here.

I will put this on "to-do" list, thanks for the suggestion.

Nick