inspect_segment: Plot VAFs across chromosomes.

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

Plot VAFs across chromosomes.

Description

Plot VAFs across chromosomes for mutations mapping to clonal simple CNAs. FIlters can be used to subset the data. Every segment has a colour, and maximum 74 segements can be plotted. The plots are split by chromosome and karyotype.

Usage

inspect_segment(
  x,
  chrs = c(paste0("chr", 1:22), "chrX", "chrY"),
  n = 200,
  l = 1000
)

Arguments

x	A CNAqc object.
chrs	The chromosome ids to use (e.g., "chr2"). All are used by default.
n	Disregard chromosomes with less than 'n' mutations mapped.
l	Disregard chromosomes that span less than 'l' nucleotide.

Value

A 'ggplot2' object.

Examples

data('example_dataset_CNAqc', package = 'CNAqc')
x = init(mutations = example_dataset_CNAqc$mutations, cna = example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)

# Deafault segments -- all chromsomes, at least 1KB, at least 200 mapped mutations.
inspect_segment(x)

# Same as above, but only for chromosome 2
inspect_segment(x, chrs = 'chr2', n = 50)

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