searchReadsPage: Get one page of reads from a GA4GH compliant server.

In adamstruck/ga4ghr: R Client for GA4GH API

Description

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

Usage

searchReadsPage(base_url,
  readGroupIds = list("MWtnLXAzLXN1YnNldDpIRzAwNTM0OkVSUjAyMDIzOA=="),
  referenceId = "R1JDaDM4LXN1YnNldDoz", 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.
readGroupIds	The read group set ID.
referenceId	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.

Details

Note that the Global Alliance for Genomics and Health API uses a 0-based coordinate system. For more detail, please see GA4GH discussions such as the following:

• https://github.com/ga4gh/schemas/issues/168

• https://github.com/ga4gh/schemas/issues/121

Value

A two-element list is returned by the function.

reads: A list of R objects corresponding to the JSON objects returned by the GA4GH Reads API.

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

See Also

Other page fetch functions: searchVariantsPage

Examples

readsPage <- searchReadsPage()
summary(readsPage)
summary(readsPage$reads[[1]])

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