I have run Absolute on tumour SNP data and I have not found an explanation of what the headers of the output files exactly mean. I would very much appreciate help to interpret the meaning of columns copy_ratio, modal_cn, subclonal and hz.
Input segmented values I have given as input to run ABSOLUTE:
Sample Chromosome Start End Num_Probes Segment_Mean
Sample1 1 82154 1222895 316 0.0342
Output from absolute:
sample Chromosome Start.bp End.bp n_probes length seg_sigma W copy_ratio modal_cn expected_cn subclonal cancer_cell_frac ccf_ci95_low ccf_ci95_high hz
34_T_SF 1 82154 1222895 316 1140741 0.00703 0.00039 0.51199 2 2.00000 0 1 1 1 0
To get copy ratio, we calculate 2^Segment_Mean, which for the probe with Segment_Mean -0.133 should be 1.0234, but ABSOLUTE computed it as 0.5 * 2 ^ Segment_Mean.
The modal_cn column represents the absolute copy number of a particular genomic location? If so, I am not sure how to interpret absolute copy number values in the context of ploidy of a cell. In case of a diploid genome, I was doing the bellow interpretation for modal_cn values:
1- heterozygous deletion
2- wt allele
But then, assuming the above interpretation is correct, how would a 5 in absolute copy number value be interpreted as? Would it be the case for aneuploid cases that have had genome doubling events, and thus have another copy of that allele?