getReadsPage: Get one page of reads from Google Genomics.

In Bioconductor/GoogleGenomics: R Client for Google Genomics API

Description

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

Usage

getReadsPage(readGroupSetId = "CMvnhpKTFhDnk4_9zcKO3_YB", chromosome = "22",
  start = 16051400, end = 16051500, fields = NULL, pageToken = NULL)

Arguments

readGroupSetId	The read group set ID.
chromosome	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

By default, this function gets reads for a small genomic region for one sample in 1,000 Genomes.

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 Google Genomics Reads API.

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

See Also

Other page fetch functions: callGRPCMethod, getSearchPage, getVariantsPage

Examples

# Authenticated on package load from the env variable GOOGLE_API_KEY.
readsPage <- getReadsPage()
summary(readsPage)
summary(readsPage$reads[[1]])

Bioconductor/GoogleGenomics documentation built on May 6, 2019, 7:51 a.m.