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hansenlab / minfi

Devel repository for minfi
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Incorporate Bayesian measurement error procedure into estimateCellCounts #194

Open sandrews5 opened 4 years ago

sandrews5 commented 4 years ago

New functionality to estimateCellCounts that will allow for eosinophil estimation in cord blood using the adult blood reference panel. Can be extended for additional cell types in the future.

kasperdanielhansen commented 4 years ago

I don't understand why there are no updates to the documentation besides a new reference. The code suggests that you're automatically doing Bayes estimation under a certain scenario. I would at a minimum expect documentation updates explaining what is happening, and I would also have expected that this could be forced-enabled/disabled by setting an option to estimateCellCounts().

sandrews5 commented 4 years ago

Thanks for the suggestions Kasper. I've added a new argument to estimateCellCounts so that the user can turn off this behavior if needed. And I've also added a short little paragraph to better explain when the function invokes the measurement error procedure.