HGVSnames: Generate genomic variant data to HGVS nomenclature

In GA4GHclient: A Bioconductor package for accessing GA4GH API data servers

Description

This function follows the official reference HGVS nomenclature. At this moment, it supports only 'substitution' and 'indel' for DNA sequences.

Usage

HGVSnames(start, ref, alt, type = "g", seqnames = NA_character_)

Arguments

start	genomic location of start
ref	reference sequence
alt	alternate sequence
type	Sequence type to be used as prefix. Allowed options are: g genomic (default); m mitochondrial; c coding DNA; n non-coding DNA.
seqnames	name of sequence (e.g. chr1, 1). It is optional.

Value

Genomic coordinates of variants formatted as HGVS nomenclature.

References

Sequence Variant Nomenclature.

Examples

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)

GA4GHclient documentation built on Nov. 8, 2020, 5:47 p.m.