plot_arm_fragmentation: Plot the arm level fragmentation test.

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Plot the arm level fragmentation test.

Description

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).

Usage

plot_arm_fragmentation(x, zoom = 0)

Arguments

x	A CNAqc object.
zoom	Number of maximum zoom panels to show in the bottom of the figure. By default 0.

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)

x = detect_arm_overfragmentation(x, genome_percentage_cutoff = .2)
plot_arm_fragmentation(x)

caravagnalab/CNAqc documentation built on Oct. 31, 2024, 3:54 a.m.