Get Integral CN from Xclone results

[Hans-0410]

Hi, XClone is a fantastic tool for analyzing Copy Number Variations from transcriptomics data. I am currently working with the results (e.g., combine_final.h5ad) and have a question regarding data extraction:

Is there a recommended way to obtain integer copy numbers (e.g., 1, 2, 3) from XClone? While I can successfully extract the probabilities for individual modules (Loss, LOH, and Gain), I need to convert these into absolute integer states for my downstream analysis. Is there a built-in function to generate an integer CNV matrix?

[James-Qiao]

Hi, thank you for the great question. XClone currently does not have integer copy number output. You can probably convert the copy number states to integer copy numbers. One way is to hard-assign the state (loss, gain, LOH) with the highest probability to be the final copy number state. Then if you only consider simple copy numbers, such as (1, 0) and (0, 1) for loss, (1, 2) and (2, 1) for gain, (2, 0) and (0, 2) for LOH, then integer copy numbers can be obtained. For more complex scenarios it becomes a much harder problem, and we haven't experimented on this.

Hope this could be helpful.

James