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UCSF-DSCOLAB / cyclone

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`prepare_checkpoint1()` could include remaining 'Data processing related' config parameters #6

Closed dtm2451 closed 2 years ago

dtm2451 commented 2 years ago

In the config file there are params...

#### Data processing related
arcsinh_cofactor: 5
subsample: FALSE
subsample_n: 4000
exclude_controls: FALSE

...but only the arcsinh transformation is part of the prepare_checkpoint1() functionality.

Potentially, could add subsampling and control exclusion.

For my use case, I am ignoring controls that were only included for batch correction purposes. I had to remove them manually from my trans_exp before running the function.

Not a huge deal, but might be nice?

Additionally, if the prepare_checkpoint1() function actually handled everything / most of what checkpoint1 does accomplish, we could maintain just prepare_checkpoint1() and plug that in to cytof_pipeline.R in place of the relevant code.

Seems like it should be fairly simple to do. I could take this work on myself if you'd like. Just let me know!

ravipatel4 commented 2 years ago

That sounds like a great idea, Dan! Please feel free to do those modifications. Thanks.