formatHgvs: Get all HGVS IDs from Vcf object.

In SuLab/myvariant.R: Accesses MyVariant.info variant query and annotation services

Description

Read in a Vcf object created by readVcf to extract all HGVS IDs for querying MyVariant.info.

Usage

formatHgvs(vcf, variant_type = c("snp", "insertion", "deletion"))

Arguments

vcf	Vcf object created by readVcf.
variant_type	Type of variant HGVS IDs to retrieve from Vcf object. Default c("snp", "insertion", "deletion")

Value

vector

References

https://myvariant.info http://www.hgvs.org/mutnomen/recs-DNA.html

See Also

formatSingleHgvs

Examples

## return HGVS IDs for all snps in a Vcf
file.path <- system.file("extdata", "dbsnp_mini.vcf", package="myvariant")
vcf <- readVcf(file.path, genome="hg19")
hgvs <- formatHgvs(vcf, variant_type="snp")

SuLab/myvariant.R documentation built on May 9, 2019, 3:22 p.m.