plot_baf_hist: Plot BAF Histogram
In Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

plot_baf_hist

R Documentation

Plot BAF Histogram

Description

This function generates a histogram of BAF (B-allele frequency) values. It supports options for adding estimated and expected peaks, area colors, and filtering homozygous calls.

Usage

plot_baf_hist(
  data_sample,
  area_single,
  ploidy,
  colors = FALSE,
  add_estimated_peaks = TRUE,
  add_expected_peaks = FALSE,
  BAF_hist_overall = FALSE,
  ratio = FALSE,
  rm_homozygous = FALSE,
  font_size = 12
)

Arguments

`data_sample`	A data.frame containing BAF and genomic position information. Must include columns 'Chr', 'Position', and 'sample'.
`area_single`	Numeric value defining the area around the expected peak to be considered.
`ploidy`	Integer or vector specifying the expected ploidy. If a vector, it must match the number of chromosomes in 'data_sample'.
`colors`	Logical. If TRUE, adds area colors to the histogram. Default is FALSE.
`add_estimated_peaks`	Logical. If TRUE, adds lines for estimated peaks. Default is TRUE.
`add_expected_peaks`	Logical. If TRUE, adds lines for expected peaks. Default is FALSE.
`BAF_hist_overall`	Logical. If TRUE, plots the BAF histogram for the entire genome. Default is FALSE.
`ratio`	Logical. If TRUE, plots the raw ratio instead of BAF. Default is FALSE.
`rm_homozygous`	Logical. If TRUE, removes homozygous calls from the histogram. Default is FALSE.
`font_size`	Numeric value for the font size of plot labels. Default is 12.