searchVariants: Get variants from a GA4GH compliant server.

In adamstruck/ga4ghr: R Client for GA4GH API

Description

This function will return all of the variants that comprise the requested genomic range, iterating over paginated results as necessary.

Usage

searchVariants(base_url, variantSetId = "MWtnLXAzLXN1YnNldDptdm5jYWxs",
  referenceName = "1", start = NULL, end = NULL, fields = NULL,
  converter = c)

Arguments

base_url	the base URL of the GA4GH server to which requests will be sent to.
variantSetId	The variant set ID.
referenceName	The chromosome.
start	Start position on the chromosome in 0-based coordinates.
end	End position on the chromosome in 0-based coordinates.
fields	A subset of fields to retrieve. The default (NULL) will return all fields.
converter	A function that takes a list of variant R objects and returns them converted to the desired type.

Details

Optionally pass a converter as appropriate for your use case. By passing it to this method, only the converted objects will be accumulated in memory. The converter function should return an empty container of the desired type if called without any arguments.

Value

By default, the return value is a list of R objects corresponding to the JSON objects returned by the GA4GH Variants API. If a converter is passed, object(s) of the type returned by the converter will be returned by this function.

See Also

searchReads for equivalent function for reads, and variantsToVRanges for a converter function.

Examples

variants <- searchVariants()
summary(variants)
summary(variants[[1]])

adamstruck/ga4ghr documentation built on May 10, 2019, 5:51 a.m.