nucmerRMD: Preprocess "nucmer" object to add group information

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

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)

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