mutStat: Plot mutation statistics for nucleiotide

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

Description

Visualization for the top mutated samples, average mutational counts, top mutated position in the genome, mutational density across the genome and distribution of mutations across countries.

Usage

mutStat(
  nucmerr = nucmerr,
  outdir = NULL,
  figure_Type = "TopMuSample",
  type_top = 10,
  country = FALSE,
  mutpos = NULL
)

Arguments

nucmerr	Mutation information containing group list(derived from "nucmer" object using "nucmerRMD" function).
outdir	The output directory.
figure_Type	Figure type for: "TopMuSample", "AverageMu", "TopMuPos", "MutDens", "CountryMutCount", "TopCountryMut".
type_top	To plot the figure involving "top n"("TopMuSample", "TopMuPos", "TopCountryMut"), the "type_top" should specify the number of objects to display.
country	To plot the figure using country as groups("CountryMutCount" and "TopCountryMut"), the "country" should be TRUE.
mutpos	If the figure type is "TopCountryMut", "mutpos" can specify A range of genomic position(eg. 28831:28931) for plot

Value

Plot the selected figure type as output.

Examples

data("nucmerr")
outdir <- tempdir()
mutStat(nucmerr = nucmerr,
        outdir = outdir,
        figure_Type = "TopCountryMut",
        type_top = 10,
        country = FALSE,
        mutpos = NULL)

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