Description Usage Arguments Value Examples
This function is to annotate the mutational events and indicate their potential effects on the proteins. Mutational events include SNP, insertion and deletion.
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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. 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. |
Write the result as ".csv" file to the specified directory.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
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