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Nanostring-Biostats / InSituType

An R package for performing cell typing in SMI and other single cell data
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bayes rule for insitutypeML #131

Closed patrickjdanaher closed 2 years ago

patrickjdanaher commented 2 years ago

In insitutype, cluster frequencies impact the loglikelihood calculation. insitutypeML should have a similar logic.

Proposal:

  1. calc logliks
  2. get cell type ID
  3. update logliks based on cell type abundances from (2). (new loglik = old loglik + log(cell type proportion)
  4. report cell type from the new logliks of (3)
patrickjdanaher commented 2 years ago

Also check that cell frequencies are being used consistently elsewhere:

patrickjdanaher commented 2 years ago

Implemented. mergeCells is not using frequencies, but it's not a problem since the logliks going into mergeCells have already incorporated frequencies.