This function produces a arm-level report for the fragmentation test, with:
* a scatter of the counts per arm, with scaled the p-values; * a jump statistics per arm, $J$, the sum of the variation in total copy number profiles, evaluated among each pair of contiguous segments.
Significantly overfragmented arms with high $J$ have a “scattered” copy number profile. Those with low $J$ are more uniform, as they show little no copy number change, and can be possibly smoothed (see below).
plot_arm_fragmentation(x, zoom = 0)Arguments
Value
A ggpubr figure
Examples
data('example_dataset_CNAqc', package = 'CNAqc')
x = init(mutations = example_dataset_CNAqc$mutations, cna = example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)
#>
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#>
#> ℹ Using reference genome coordinates for: GRCh38.
#> ✔ Found annotated driver mutations: TTN, CTCF, and TP53.
#> ✔ Fortified calls for 12963 somatic mutations: 12963 SNVs (100%) and 0 indels.
#> ! CNAs have no CCF, assuming clonal CNAs (CCF = 1).
#> ✔ Fortified CNAs for 267 segments: 267 clonal and 0 subclonal.
#> ✔ 12963 mutations mapped to clonal CNAs.
x = detect_arm_overfragmentation(x, genome_percentage_cutoff = .2)
#> ℹ One-tailed Binomial test: 8 tests, alpha 0.01. Short segments: 0.2% of the reference arm.
#> ✔ chr7p, p = 1.7179869184e-24 ~ 34 segments, 34 short.
#> ✔ chr1p, p = 1.62738995200002e-15 ~ 24 segments, 23 short.
#> ✔ chr11q, p = 2.4788992e-07 ~ 14 segments, 12 short.
#> ✔ chr1q, p = 4.34176000000001e-08 ~ 13 segments, 12 short.
#> ✔ chr12q, p = 4.34176000000001e-08 ~ 13 segments, 12 short.
#> ✔ chr3q, p = 4.52608e-06 ~ 12 segments, 10 short.
#> ✔ chr7q, p = 4.52608e-06 ~ 12 segments, 10 short.
#> ✔ chr8p, p = 9.21599999999998e-07 ~ 11 segments, 10 short.
#> ℹ 8 significantly overfragmented chromosome arms (alpha level 0.01).
plot_arm_fragmentation(x)
