Hi there,
I am looking at ABSOLUTE CN calls from this file: DepMap Data Downloads
I am a little confused with regards to how to interpret the columns labeled “Cancer_call_frac_a1” and “Cancer_cell_frac_a2” with regards to how they relate to the “Modal_HSCN_1” and “Modal_HSCN_2” columns, respectively. “Cancer_call_frac_a1” describes “Max. posterior estimate of fraction of sample’s cells containing somatic copy number change of allele 1”, while “Modal_HSCN_1” describes “minor (alt) allele ABSOLUTE copy number call.” So does “Cancer_call_frac_a1” describe the fraction of a sample’s cells that have a copy number equivalent to “Modal_HSCN_1”, or that are different from “Modal_HSCN_1”?
I was also wondering why the range of values for the “Subclonal_HSCN_a1” and “Subclonal_HSCN_a2” columns is only 0-1 while the range of values goes from 0-7 for the “Modal_HSCN_1” and “Modal_HSCN_2” columns?
My goal is to identify genomic regions that have a ABSOLUTE copy number of 1 for both the major and minor alleles (i.e. diploid regions). Previously, I identified those regions as rows that have “Modal_HSCN_1” == 1 AND “Modal_HSCN_2” == 1, but I am wondering if I need to take some of the other columns into consideration.
I appreciate your help and all the work done!
Best,
Elaine
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