Thank you for this tool to summarize the copy number for multiple sample. It works great!
I got a question. In my CNV analysis for loss, we have only deletion or deep deletion, which is 1 or 0 and normal pliody is 2.
In the plot for percentage of copy number gain or loss, I believe you kept normal ploidy as 0 instead of 2, and any gain should be > 0 and loss/ deletion will be less than 0. But here, I see the ploidy values -3, -4 etc. Can you please explain how this values came? Please correct me if my understanding is wrong.
Hi,
Thank you for this tool to summarize the copy number for multiple sample. It works great! I got a question. In my CNV analysis for loss, we have only deletion or deep deletion, which is 1 or 0 and normal pliody is 2. In the plot for percentage of copy number gain or loss, I believe you kept normal ploidy as 0 instead of 2, and any gain should be > 0 and loss/ deletion will be less than 0. But here, I see the ploidy values -3, -4 etc. Can you please explain how this values came? Please correct me if my understanding is wrong.
Thanks Parvathi.