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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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Correct integer copy number for high-level events and for chrX (males) #41

Closed gavinha closed 5 years ago

gavinha commented 6 years ago

Include feature to correct integer copy number for two purposes:

  1. High-level copy number events higher than maxCN state.
    This will help to adjust absolute integer copy number beyond the modeled copy number states.
  2. Adjust chrX integer copy number results for males. ChrX for males have a baseline of 1 copy and the results do not reflect this in the absolute copy number predictions reported.

This also address issue #28

I will use a nearly identical method recently added to TitanCNA. See the invocation and function declaration for reference.

https://github.com/gavinha/TitanCNA/blob/49081fb7334ce7b5988c52b6eb9953dfe2743d1f/scripts/R_scripts/titanCNA.R#L271-L272

https://github.com/gavinha/TitanCNA/blob/49081fb7334ce7b5988c52b6eb9953dfe2743d1f/R/utils.R#L1168-L1169