globalSNPprofile function

Global single nucleotide polymorphism (SNP) profiling in virus genome

Global single nucleotide polymorphism (SNP) profiling in virus genome

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

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.

Returns

Plot the selected figure type as output.

Examples

data("nucmerr") outdir <- tempdir() globalSNPprofile(nucmerr = nucmerr, outdir = outdir, figure_Type = "heatmap", country = "global", top = 5)
  • Maintainer: Shaoqian Ma
  • License: Artistic-2.0
  • Last published: 2020-09-18