search_variants: Search for Variants

Description Usage Arguments Examples

View source: R/search.R

Description

Search for Variants

Usage

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search_variants(client, variant_set_id, call_set_ids = NULL,
  reference_name = NULL, start = NULL, end = NULL, page_size = NULL,
  page_token = NULL)

Arguments

client

A ga4gh_client object

variant_set_id

The ID of the Variant Set to search within

call_set_ids

A list of Call Set IDs. Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.

reference_name

Only return variants on this reference.

start

The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length.

end

The end of the window (0-based, exclusive) for which overlapping variants should be returned.

page_size

Specifies the maximum number of results to return in a single page. If unspecified, the client default will be used.

page_token

The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.

Examples

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ref_client <- ga4gh_client("http://1kgenomes.ga4gh.org", api_location = "")

## Not run: 
library(magrittr)
## Find a dataset to search in
datasets <- ref_client %>% search_datasets() %>% content()
d_id <- datasets$datasets[[1]]$id

## Find a variant set to search in
variant_sets <- ref_client %>% search_variant_sets(d_id) %>% content()
vs_id <- variant_sets$variantSets[[1]]$id

## Search for variants in the variant set
variants <- ref_client %>% search_variants(vs_id, reference_name = "1") %>%
 content()
variants$variants[[1]]

## End(Not run)

Rga4gh documentation built on May 29, 2017, 9:12 a.m.