globalSNPprofile: Global single nucleotide polymorphism (SNP) profiling in...

In CovidMutations: Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019)

Description

This function is to visualize the global SNP pattern in the SARS-CoV-2 genome.

Usage

globalSNPprofile(
  nucmerr = nucmerr,
  outdir = NULL,
  figure_Type = "heatmap",
  country = "global",
  top = 5
)

Arguments

nucmerr	Mutation information containing group list(derived from "nucmer" object using "nucmerRMD" function).
outdir	The output directory.
figure_Type	Figure type for either "heatmap" or "count".
country	Choose a country to plot the mutational pattern or choose "global" to profile mutations across all countries. The default is "global".
top	The number of mutational classes to plot.

Value

Plot the selected figure type as output.

Examples

data("nucmerr")
outdir <- tempdir()
globalSNPprofile(nucmerr = nucmerr,
                 outdir = outdir,
                 figure_Type = "heatmap",
                 country = "global",
                 top = 5)

CovidMutations documentation built on Sept. 18, 2020, 5:06 p.m.