search_reference_bases: Search for Reference Bases

In Rga4gh: An Interface to the GA4GH API

Description

Search for Reference Bases

Usage

search_reference_bases(client, reference_id = NULL, start = NULL,
  end = NULL, page_size = NULL, page_token = NULL)

Arguments

client	A ga4gh_client object
reference_id	The ID of the Reference to search within
start	The start position (0-based) of this query. Defaults to 0. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).
end	The end position (0-based, exclusive) of this query. Defaults to the length of this Reference
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 reference set to search in
reference_sets <- ref_client %>% search_reference_sets() %>% content()
rs_id <- reference_sets$referenceSets[[1]]$id

## Find a reference to search in
references <- ref_client %>% search_references(rs_id) %>% content()
ref_id <- references$references[[1]]$id

## Find a string of bases from 10000 -> 11000
reference_bases <- ref_client %>%
 search_reference_bases(ref_id, start = 10000, end = 11000) %>% content()
reference_bases

## End(Not run)

Rga4gh documentation built on May 1, 2019, 6:35 p.m.