search_variant_annotations: Search for Variant Annotations

Description Usage Arguments Examples

View source: R/search.R

Description

Search for Variant Annotations

Usage

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search_variant_annotations(client, variant_annotation_set_id,
  reference_id = NULL, reference_name = NULL, start = NULL, end = NULL,
  effects = NULL, page_size = NULL, page_token = NULL)

Arguments

client

A ga4gh_client object

variant_annotation_set_id

The ID of the Variant Annoation Set to search within.

reference_id

Only return variants with reference alleles on th reference with this ID. One of this field or referenceName is required.

reference_name

Only return variants with reference alleles on the reference with this name. One of this field or referenceId is required.

start

The beginning of the window (0-based, inclusive) for which variants with overlapping reference alleles should be returned. 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 of the window (0-based, exclusive) for which variants with overlapping reference alleles should be returned.

effects

A data.frame with columns id, sourceName, sourceVersion, term. This filter allows variant, transcript combinations to be extracted by effect type(s). Only return variant annotations including any of these effects and only return transcript effects including any of these effects. Exact matching across all fields of the Sequence Ontology OntologyTerm is required. (A transcript effect may have multiple SO effects which will all be reported.) If empty, return all variant annotations.

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: 
## 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$variantSets[[2]]$id

## Find a variant annotation set to search in
variant_annotation_sets <- ref_client %>%
 search_variant_annotation_sets(vs_id) %>% content()
vas_id <- variant_annotation_sets$variantAnnotationSets[[1]]$id

## Search for variant annotations in the variant annotation set
variant_annotations <- ref_client %>%
 search_variant_annotations(vas_id, reference_name = "1") %>% content
variant_annotations$variantAnnotations[[1]]

## End(Not run)

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