# helper function ---------------------------------------------------------
convert_to_seq <- function(dna.seq){
seq <- lapply(as.character(dna.seq), function(x) {
splitseq(s2c(x))
})
return(seq)
}
extract_region <- function(object, check.region){
if (!check.region) {
seq <- convert_to_seq(object@dnaseq)
seq.region <- mapply(function(x, y) {
return(x[y])
}, seq, object@region, SIMPLIFY = FALSE)
} else {
seq.region <- lapply(as.character(object@dnaseq),
function(x) {
splitseq(s2c(x))
})
}
return(seq.region)
}
region_back <- function(seq.mut, check.region, seq, object){
if (!check.region) {
seq.mut <- mapply(function(x, y, z) {
x[y] <- z
return(x)
}, seq, object@region, seq.mut, SIMPLIFY = FALSE)
}
seq.mut <- Biostrings::DNAStringSet(unlist(lapply(seq.mut, c2s)))
return(seq.mut)
}
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