search_variants: Search for Variants

In Rga4gh: An Interface to the GA4GH API

Description

Search for Variants

Usage

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

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 1, 2019, 6:35 p.m.