Plot bin-level log2 coverages and segmentation calls together. Without any further arguments, this plots the genome-wide copy number in a form familiar to those who have used array CGH.
Bin-level log2 ratios (.cnr)
Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
| chromosome | Genomic chromosome (e.g., chr1, chrX) |
| start | Start position of the bin. |
| end | End position of the bin. |
| gene | Gene name(s) overlapping the bin (if applicable). |
| log2 | Normalized log2 ratio (sample coverage / reference coverage). |
| depth | Average read depth in the bin. |
| weight | Reliability weight of the bin (higher = more reliable). |
Segmented log2 ratios (.cns)
Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
| chromosome | start, end: Genomic coordinates of the segment |
| gene | Gene(s) overlapping the segment. |
| log2 | Mean log2 ratio of the segment. |
| probes | Mean log2 ratio of the segment. |
| depth | Average read depth. |
| weight | Reliability weight. |
| p_value | Statistical confidence (lower = more significant). |