search_reference_bases: Search for Reference Bases

Description Usage Arguments Examples

View source: R/search.R

Description

Search for Reference Bases

Usage

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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

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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 29, 2017, 9:12 a.m.