Open yashcrux opened 6 months ago
The -t command-line parameter is indeed somewhat related to tumor purity, ploidy and subclonality. To have maximum flexibility, I so far opted for a simple command-line parameter that determines the min. copy-number shift for the segmentation and somatic classification. For instance, for a diploid tumor with 80% tumor purity, a clonal genomic rearrangement of copy-number 3 would be observed at CN 2.8 = 0.8 3 + 0.2 2 so you can put a very stringent threshold of -t 0.5. However, for a tetraploid tumor with 30% tumor purity, a clonal genomic rearrangement of copy-number 5 would be observed at CN 4.3 = 0.3 5 + 0.7 4 so you need to use a very lenient cutoff such as -t 0.2 to detect such a shift in copy-number from 4 to 5.
Hi Tobias.
Thanks for this explanation! Also can you please help me understand the relation of CN with -t.
Like what range should I consider to set, in this case, -t 0.5 when CN 2.8 or the other case. in my case: I have 2 tumor subtypes : 1st type: the values of CN ranges from 2.5 to 2.95 2nd type: ...CN 3.39 to 3.96
HI Tobias
I read the explanation again and decided on the -t values for : 1st type - 0.5 2nd type - 0.3
I don't know if its correct or I am in the right direction of the understanding of your explanation
Thanks in advance
Hi
I had a question regarding how the tumor purity values are parsed while somatic CNA. I understand its by using '-t'. I don't understand whether it takes it in percentage or decimal.
For example if the purity is 88%, it shuld be introduced as "-t 88" or "-t 0.88"
Thanks for the help!