makeVCFFromGA4GHResponse: makeVCFFromGA4GHResponse function

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

Description

Convert DataFrame output from searchVariants and getVariant functions to VCF class.

Usage

makeVCFFromGA4GHResponse(variants)

Arguments

variants

DataFrame generated by searchVariants.

Value

VCF object.

See Also

searchVariants, getVariant, VCF, DataFrame

Examples

host <- "http://1kgenomes.ga4gh.org/"
## Not run: 
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariants(host, variantSetId, referenceName = "1",
    start = 15000, end = 16000)
variants

makeVCFFromGA4GHResponse(variants)

## End(Not run)

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