Would be nice to have a few functions for filtering count tables

sterrettJD / HoMiStats

Statistics for host-microbiome dual transcriptomics

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Open sterrettJD opened 7 months ago

sterrettJD commented 7 months ago

For example,

Tagging in @jboconnor13 in case you'd like to contribute any of these!

jboconnor13 commented 7 months ago

Maybe it might be worth it to remove constant features as well?

sterrettJD commented 7 months ago

[ ] removal of features that correlate with % host reads removed from a sample (https://forum.biobakery.org/t/need-for-human-sequences-in-chocophlan-database/5749) or maybe these should just be included in the model?

sterrettJD commented 7 months ago

Implemented the following in the HoMiCorr branch for testing on real data: removal of low-variance features removal of low-count features