mergeEvents {CovidMutations}

Merge neighboring events of single nucleotide polymorphism (SNP), insertion and deletion.

Description

The first step for handling the nucmer object, then effects of mutations can be analysed using "indelSNP" function.

Usage

mergeEvents(nucmer = nucmer)

Arguments

nucmer

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

Value

An updated "nucmer" object.

Examples

#The example data:
data("nucmer")
#options(stringsAsFactors = FALSE)

#The input nucmer object can be made by the comment below:
#nucmer<-read.delim("nucmer.snps",as.is=TRUE,skip=4,header=FALSE)
#colnames(nucmer)<-c("rpos","rvar","qvar","qpos","","","","",
#"rlength","qlength","","","rname","qname")
#rownames(nucmer)<-paste0("var",1:nrow(nucmer))

# Fix IUPAC codes
nucmer<-nucmer[!nucmer$qvar%in%c("B","D","H","K","M","N","R","S","V","W","Y"),]
nucmer<- mergeEvents(nucmer = nucmer)## This will update the nucmer object