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mskilab-org / dryclean

Irons out wrinkles in noisy coverage data using robust PCA
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could not find function "identify_germline" #12

Open Bio-LiHe opened 1 year ago

Bio-LiHe commented 1 year ago

Hi I run the following code 

grm = identify_germline(normal.table.path = "~/git/dryclean/inst/extdata/normal_table.rds", path.to.save = "~/git/dryclean/inst/extdata/", signal.thresh=0.5, pct.thresh=0.98)

get an error

could not find function "identify_germline"

Has identify_germline been discarded? Do it still need the step of Identifying germline events?

pblaney commented 1 year ago

Hi @Bio-LiHe

You likely have already found this out but that command has been deprecated. It is now included in the prepare_detergent() function.

I am currently testing the workflow but based on the output detergent.rds file, it appears the germline event inference has correctly taken place.

Hope this helps but the authors may have more to say on the matter.

Best, Patrick