Description Usage Arguments Value Examples
The first step for handling the nucmer object, then effects of mutations can be analysed using "indelSNP" function.
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nucmer |
An object called "nucmer", mutation information derived from "nucmer.snp" variant file by "seqkit" software and "nucmer SNP-calling" scripts. |
An updated "nucmer" object.
1 2 3 4 5 6 7 8 9 10 11 12 13 | #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
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