nucmerRMD {CovidMutations}

Preprocess "nucmer" object to add group information

Description

Manipulate the "nucmer" object to make the analysis easier.

Usage

nucmerRMD(nucmer = nucmer, outdir = NULL, chinalist = chinalist)

Arguments

nucmer

An object called "nucmer", mutation information derived from "nucmer.snp" variant file by "seqkit" software and "nucmer SNP-calling" scripts.

outdir

The output directory.

chinalist

A list of places in China, for displacing some original cities with "China" in order to make the downstream analysis easier.

Value

Saving the updated "nucmer" object.

Examples

data("nucmer")
data("chinalist")
#outdir <- tempdir()
nucmerr<- nucmerRMD(nucmer = nucmer, outdir = NULL, chinalist = chinalist)