Calculating HRD score
Has anyone successfully calculated the HRD score (using nTAI, LOH, and LST)? I tried using the script provided in this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443545/) but it does not seem to work. Specifically, there is a function "check.names" that references an 11th column of a matrix that isn't required by the program (which requires a 10 column matrix).
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Do you need to use that script specifically? If you just want to calculate HRD scores, there is also scarHRD, which worked well in my experience: https://github.com/sztup/scarHRD
Please share the link to code or host the code some where else and share the link (if that is okay with authors). Please also provide input file example.
Has anyone an update about the script provided in the paper. I am getting the same error. Has anyone figured out a solution? Thank you in advance!