Table 12.
Features of the final SCNA calling using modified settings for TitanCNA
| Chrom | loc.start | loc.end | num.mark | seg.mean | copynumber | minor_cn | major_cn |
|---|---|---|---|---|---|---|---|
| 1 | 946247 | 18088176 | 260 | 0.332 | 4 | 2 | 2 |
| 1 | 18088177 | 3918;l4262 | 225 | −0.641 | 2 | 0 | 2 |
| 1 | 39184263 | 153463863 | 525 | 0.318 | 4 | 2 | 2 |
| 1 | 153463864 | 170755470 | 230 | 0.265 | 4 | 0 | 4 |
| 1 | 170755471 | 170958981 | 1 | 0.47 | 6 | 2 | 4 |
Here is a preview of the generated CRCTumorOA1_nclones1.TitanCNA.segments.txt file. It consists of the segmented genome of sample CRCTumorOA1 based on using the corrected settings for maximum integer copy number. It allows estimation of copy number for extremely high gains. Here the corrected integer copy number is set to 14, assuming the genome is haploid with regards to Chromosomes X and Y. Therefore, there are some regions that require correction of chromosomal state.