getVariant: getVariant function

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

Description

Get a variant by its ID with all call sets for this variant.

Usage

getVariant(host, variantId, asVCF = TRUE)

Arguments

host	URL of GA4GH API data server.
variantId	The ID of the Variant to be retrieved.
asVCF	If TRUE the function will return an VCF with header (default), otherwise it will return an DataFrame.

Details

This function requests GET host/variants/variantId.

Value

VCF object (when asVCF = TRUE) or DataFrame object (otherwise).

References

Official documentation.

See Also

DataFrame, searchVariants, searchVariantsByGRanges, VCF, makeVCFFromGA4GHResponse

Examples

host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variantId <- searchVariants(host, variantSetId, "1", 15031, 15031)$id
getVariant(host, variantId)

getVariant(host, variantId, asVCF = FALSE)

## End(Not run)

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