squaresplot: Plot Battenberg copy number solutions for a segment

In shaghayeghsoudi/Battenberg_customized: Battenberg subclonal copy number caller

Description

squaresplot plots the different Battenberg copy number solutions for a segment

Usage

squaresplot(
  tumourname,
  run_dir,
  segment_chr,
  segment_pos,
  platform_gamma = 1,
  pdf = 0,
  binwidth_baf = 0.25,
  xylimits = c(-0.2, 5)
)

Arguments

tumourname	Sample name
run_dir	Running directory
segment_chr	Chromosome containing the segment to be investigated
segment_pos	Chromosomal position within the segment in Mb (e.g. 90M)
platform_gamma	Platform-specific gamma value (0.55 for SNP6, 1 for NGS), default 1
pdf	Output format: 0 for png (default), 1 for pdf
binwidth_baf	BAF isobafline spacing, default 0.25
xylimits	x/y-axis limits, default c(-0.2,5)

Details

The plot is output to the run directory as "tumourname_squares_chr_position.png/pdf"

Author(s)

jd

shaghayeghsoudi/Battenberg_customized documentation built on Feb. 13, 2022, 4:10 a.m.