HGVSnames {GA4GHclient}R Documentation

Generate genomic variant data to HGVS nomenclature

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)

[Package GA4GHclient version 1.12.0 Index]