search_features: Search for Features

Description Usage Arguments Examples

View source: R/search.R

Description

Search for Features

Usage

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search_features(client, feature_set_id = NULL, parent_id = NULL,
  feature_types = NULL, reference_name = NULL, gene_symbol = NULL,
  name = NULL, start = NULL, end = NULL, page_size = NULL,
  page_token = NULL)

Arguments

client

A ga4gh_client object

feature_set_id

The ID of the Feature Set to search within. Either feature_set_id or parent_id must be non-null.

parent_id

Restricts the search to direct children of the given parent feature ID. Either feature_set_id or parent_id must be non-null.

feature_types

A list of feature types. If specified, this query matches only annotations whose feature_type matches one of the provided ontology terms.

reference_name

Only return features on the reference with this name

gene_symbol

Only return features with matching the provided gene symbol (case-sensitive, exact match).

name

Only returns features with this name (case-sensitive, exact match).

start

The beginning of the window (0-based, inclusive) for which overlapping features 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 features 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 feature set to search in
feature_sets <- ref_client %>% search_feature_sets(d_id) %>% content()
fs_id <- feature_sets$featureSets[[1]]$id

## Search the for features in the feature set
features <- ref_client %>% search_features(fs_id) %>% content()
features$features[[1]]


## End(Not run)

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