HGVSnames: Generate genomic variant data to HGVS nomenclature

Description Usage Arguments Value References Examples

View source: R/HGVSnames.R

Description

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

Usage

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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

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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.