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Please, can you help me with a confusion?

In whole genome sequencing, if

Total copy number (major + minor allele copy number by SCAT R package) for SMAD4 in a sample = 4

Th estimated ploidy by SCAT for this sample = 4.043696

So, the segment mean (required for GISTIC) for SMAD4 for this given position of genome in the given sample = log2(4/4.043696) = -0.01567461

We can consider this as a loss of copy number for SMAD4

But with GISTIC threshold -td = 0.1 this is neutral copy number change (if I am not wrong)

So, If I want to ask GISTIC to give me

amplification: copy number ≥2 × average ploidy​
gain:  copy number >1.25 × average ploidy
loss: copy number <0.75 ×average ploidy
deletion: copy number 0

If I put -ta = 1.25 and -td = 0.75 , do I achieve the above?

I am seriously struggling with this intuition of relationship between segment mean and GISTIC copy number threshold

Thank you for any help

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    $\begingroup$ You've invested quite the effort in this question, Angel. I hope this gets answered soon and answered well. Cheers! $\endgroup$ – Ram RS Mar 25 at 15:54

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