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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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--alpha does not set up gridalpha[] properly #13

Closed wac closed 6 years ago

wac commented 6 years ago

It appears the assumption in the code is that gridAlpha[0] = 0.0. When using --alpha to set the alpha values, you will need to do

--alpha 0.0 --alpha 0.5

Otherwise doublet detection is broken. Just doing

--alpha 0.5

(as recommended in the help) causes no alpha values to ever be tested for doublets (the first alpha value never gets tested for doublets). Probably need to check/enforce gridAlpha[0]=0.0.

Symptom is getting very weird doublet calls since jBest, kBest end up being set to -1.

Current workaround is to make sure you always use --alpha 0.0 before specifying the actual alpha values you want to test.

yimmieg commented 6 years ago

thanks, we have updated the help to reflect this.