searchVariantsPage: Get one page of variants from a GA4GH compliant server.

In adamstruck/ga4ghr: R Client for GA4GH API

Description

In general, use the getVariants method instead. It calls this method, returning variants from all of the pages that comprise the requested genomic range.

Usage

searchVariantsPage(base_url, variantSetId = "MWtnLXAzLXN1YnNldDptdm5jYWxs",
  referenceName = "1", start = NULL, end = NULL, fields = NULL,
  pageToken = NULL)

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.
pageToken	The page token. This can be NULL (default) for the first page.

Value

A two-element list is returned by the function.

variants: A list of R objects corresponding to the JSON objects returned by the GA4GH Variants API.

nextPageToken: The token to be used to retrieve the next page of results, if applicable.

See Also

Other page fetch functions: searchReadsPage

Examples

variantsPage <- getVariantsPage()
summary(variantsPage)
summary(variantsPage$variants[[1]])

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