Plot allele-specific copy number segments (absolute copies)

Function that plots allele-specific copy number segments (minor + total allele copies)

Usage

plot_cna_segments_absolute(
  chrom_coordinates = NULL,
  cna_segment = NULL,
  cna_gene = NULL,
  tumor_ploidy = 2,
  amp_threshold_effective = 5,
  threshold_mode = "absolute",
  gain_threshold_effective = 3,
  del_threshold_effective = 1,
  color_palette = pcgrr::color_palette
)

Arguments

chrom_coordinates

data frame with assembly-specific chromosome coordinate data (length etc)

cna_segment

data frame with annotated copy number segments

cna_gene

data frame with gene-level copy number data

tumor_ploidy

numeric tumor ploidy used as the neutral baseline. A dotted reference line is always drawn at this value. Default 2.

amp_threshold_effective

numeric effective amplification threshold in absolute copy number units. A dotted reference line is drawn at this value when threshold_mode is "absolute" or "combined". Default 5.

threshold_mode

character thresholding mode applied to all CNA tiers: "absolute", "relative", or "combined". The amplification threshold line is shown only when mode is "absolute" or "combined". Default "absolute".

gain_threshold_effective

numeric effective gain threshold in absolute copy number units. A dotted reference line is drawn at this value. Default 3.

del_threshold_effective

numeric effective heterozygous deletion threshold in absolute copy number units. A dotted reference line is drawn at this value. Default 1.