Absolute copy number estimation from low-coverage whole genome sequencing
This package uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers. For this it uses segmented data from the QDNAseq package, which in turn uses a number of dependencies to turn mapped reads into segmented data. ACE will run QDNAseq or use its output rds-file of segmented data. It will subsequently run through all samples in the object(s), for which it will create individual subdirectories. For each sample, it will calculate how well the segments fit (the relative error) to integer copy numbers for each percentage of tumor cells (cells with divergent segments).
| System | Target | Derivation | Build status |
|---|---|---|---|
| x86_64-linux | /gnu/store/gzs0f0ad1knqbps9rkmsykladrzm0vlp-r-ace-1.14.0.drv | ||
| i686-linux | /gnu/store/svgc2n4s0fr6jbn8kwdcj6m56i17hvlx-r-ace-1.14.0.drv |
| Linter | Message | Location |
|---|---|---|
| No lint warnings ✓ | ||