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 =
ploidy by SCAT for this sample =
segment mean (required for GISTIC) for SMAD4 for this given position of genome in the given sample = log2(4
We can consider this as a
loss of copy number for SMAD4
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