indelSNP {CovidMutations}

Provide effects of each single nucleotide polymorphism (SNP), insertion and deletion in virus genome

Description

This function is to annotate the mutational events and indicate their potential effects on the proteins. Mutational events include SNP, insertion and deletion.

Usage

indelSNP(
  nucmer = nucmer,
  saveRda = FALSE,
  refseq = refseq,
  gff3 = gff3,
  annot = annot,
  outdir = NULL
)

Arguments

nucmer

An object called "nucmer", mutation information derived from "nucmer.snp" variant file by "seqkit" software and "nucmer SNP-calling" scripts. To be processed by "indelSNP" function, The nucmer object should be first transformed by "mergeEvents" function.

saveRda

Whether to save the results as ".rda" file.

refseq

SARS-Cov-2 genomic reference sequence.

gff3

"GFF3" format annotation data for SARS-Cov-2.

annot

Annotation of genes(corresponding proteins) list from "GFF3" file by "setNames(gff3[,10],gff3[,9])".

outdir

The output directory.

Value

Write the result as ".csv" file to the specified directory.

Examples

data("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
data("refseq")
data("gff3")
annot <- setNames(gff3[,10],gff3[,9])
#outdir <- tempdir()
nucmer<- indelSNP(nucmer = nucmer,
                  saveRda = FALSE,
                  refseq = refseq,
                  gff3 = gff3,
                  annot = annot,
                  outdir = NULL)