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mskilab-org / dryclean

Irons out wrinkles in noisy coverage data using robust PCA
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apply dryclean to other ASCN algoritms #4

Closed jinghu23 closed 2 years ago

jinghu23 commented 3 years ago

Hi, you guys did great jobs on this. I just want to feed the corrected rds data to other ASCN algoritms like sequenza. Btw, I noticed that you mentioned in the paper that output of dryclean could be fed to more spphiscated segmentation algorithms. Could u give me an example? Thx in advance!

Jay

asd1289 commented 3 years ago

Hi Jay,

Sorry for the delayed response. So I would suggest treating dryclean output as your standard practice tumor-normal output. Given this, you can modify the column names, etc for the GRanges to fit the ASCN algorithm input requirements. Additionally you can use segnmentation algorithms like CBS by just log-transforming the "foreground" column from dryclean. Hope this helps.

asd1289 commented 2 years ago

We have recently used dryclean output to replace FACET total copy number inputs and it seems to work. Hopefully this has been helpful and I am closing this issue.