plot6mutationSpectrumFromVcf: plot6mutationSpectrumFromVcf

In FunGeST/Palimpsest: Package

plot6mutationSpectrumFromVcf

Description

Function to plot the proportions of each of the 6 substitution types from a vcf file (containing one or a series of samples)

Usage

plot6mutationSpectrumFromVcf(
  vcf,
  sample.col = "sample",
  substype.col = "substype",
  averageProp = FALSE,
  plot.file = NULL
)

Arguments

vcf	vcf data frame containing the mutations
sample.col	Sample column name in vcf
substype.col	Substitution types column name in vcf
averageProp	If TRUE, the proportions returned will be the average of sample-wise proportions, otherwise the general proportion over the vcf is used (induces slight changes)
plot.file	File to which the plot should be saved (if left NULL, plot will be sent directly to the active window)

FunGeST/Palimpsest documentation built on June 2, 2024, 4:21 a.m.