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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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PC1 of one chr is chromosome arm #31

Closed csijcs closed 2 years ago

csijcs commented 2 years ago

Great tool!

I came across one issue. For a particular sample the PC1 is the comaprtment score for all chrs except one. For that chr PC1 came out as the chromosome arms. Is there an easy way to get PC2 for that chr only?

For all other chrs and for samples PC1 is accurate.

ay-lab commented 2 years ago

Thank you for the kind words! Have you looked at reselectpc.r (under /utility)? You can see more about it on this wiki page.

csijcs commented 2 years ago

Sorry, I didn't realize there was a "new" way of doing it. I was still doing it the "old" way (dchic.py). I will run through the new protocol/documentation. Out of curiosity, is there any way to recover PC2 from the old way?

ay-lab commented 2 years ago

I don't recall there being an explicit way to force it. The differential calling scripts draw from the XX.PC.coordinates.txt file, though, so you could grab PC2 from the R files (keep intermediates) and then manually change them there.