PPplots: Plot bin and het copy number histogram as well as a contour...

In mskilab/skitools: Various mskilab R utilties

Plot bin and het copy number histogram as well as a contour plot for allele fractions.

Description

Plot bin and het copy number histogram as well as a contour plot for allele fractions.

Usage

PPplots(
  cov,
  hets,
  pu,
  pl,
  somatic_vars = NA,
  xmax = 10,
  hist_breaks = 10000,
  outputdir = ".",
  prefix = "",
  suffix = "",
  N_subsample = 10000
)

Arguments

cov	bin coverage depth
hets	het_pileup
pu	purity
pl	ploidy
xmax	maximum value for x-axis of histograms
outputdir	output directory for plots
prefix	a prefix to use for output plots
suffix	a suffix to use for output plots
N_subsample	How many entries to randomly sample from hets when generating the contour plot

Author(s)

Alon Shaiber histogram of bin copy number histogram of het copy numbers density plots for hets

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.