getVariantsPage {GoogleGenomics}R Documentation

Get one page of variants from Google Genomics.

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

getVariantsPage(variantSetId = "10473108253681171589", chromosome = "22",
  start = 16051400, end = 16051500, fields = NULL, pageToken = NULL)

Arguments

variantSetId

The dataset 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 variants from a small section of 1000 Genomes phase 1 variants.

Value

A two-element list is returned by the function.

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

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

See Also

Other page fetch functions: callGRPCMethod, getReadsPage, getSearchPage

Examples

# Authenticated on package load from the env variable GOOGLE_API_KEY.
variantsPage <- getVariantsPage()
summary(variantsPage)
summary(variantsPage$variants[[1]])

[Package GoogleGenomics version 2.2.0 Index]