I try to explain in the most just way possible the different modes of the call function.
Please tell me if I am wrong and complete the information if necessary.
The call function allows the estimation of the absolute number of copies for each segment. There are two modes of calculation:
- the threshold mode which establishes a threshold scale for categorizing log2. By specifying 4 thresholds, we obtain 5 categories: OX, 1X, 2X 3X and 4X +
- mode that takes ploidy into account (clonal) It estimates a relationship between the ploidy of each chromosome and the log2 of the segments. By default the ploidy is 2X for autosomes.
I still have questions:
- How is the basic value of the clonal mode set? Based on the log2 average of the chromosome? Based on the log2 average of the entire sample? By another way (which)?
- How is it decided afterwards that the sample contains a deletion or a duplication? Are these thresholds? A proportionality calculation (and a rounding)?
- The clonal mode is rather used for pure somatic samples or on the contrary with 20-80% of tumor cells or even less?
- Threshold mode is used instead for pure somatic samples or on the contrary with 20-80% tumor cells or even less?
- the fact of rescalling the sample makes it possible to use one mode rather than another? What is the limit? (Sometimes we have samples with 5% of tumor cells and I have the impression that rescalling creates more noise than real call.)
Thank you for your tool, your community and the responsiveness of your answers (which are very rewarding). For all of these reasons we decided to use your tool for the detection of CNV routinely in our laboratory.