HGVSnames {GA4GHclient} | R Documentation |
This function follows the official reference HGVS nomenclature. At this moment, it supports only 'substitution' and 'indel' for DNA sequences.
HGVSnames(start, ref, alt, type = "g", seqnames = NA_character_)
start |
genomic location of start |
ref |
reference sequence |
alt |
alternate sequence |
type |
Sequence type to be used as prefix. Allowed options are:
|
seqnames |
name of sequence (e.g. chr1, 1). It is optional. |
Genomic coordinates of variants formatted as HGVS nomenclature.
Sequence Variant Nomenclature.
start <- c(45576, "88+1", 6775, 6775, 145, 9002, 4, 12345611, 58347698) ref <- c("A", "G", "T", "TCA", "CGA", "AAAAAAAA", "GC", "G", "A") alt <- c("C", "T", "GA", "C", "TGG", "TTT", "TG", "A", "*") type <- c("g", "c", "g", "g", "c", "g", "g", "g", "g") seqnames <- c("", "", NA, NA, NA, NA, NA, "chr11", NA) HGVSnames(start, ref, alt, type, seqnames)