search_phenotypes: Search for Phenotypes

Description Usage Arguments Examples

View source: R/search.R

Description

Search for Phenotypes

Usage

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search_phenotypes(client, phenotype_association_set_id = NULL,
  description = NULL, id = NULL, qualifiers = NULL, type = NULL,
  age_of_onset = NULL, page_size = NULL, page_token = NULL)

Arguments

client

A ga4gh_client object

phenotype_association_set_id

The ID of Phenotype Association Set to search within

description

String

id

String

qualifiers

A data.frame with columns id, sourceName, sourceVersion, term.

type

A named list with names id, sourceName, sourceVersion, term. Only return results that match this type

age_of_onset

A named list with names id, sourceName, sourceVersion, term. Only return results that match this age_of_onset

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 phenotype association set to search in
phenotype_association_sets <- ref_client %>%
 search_phenotype_association_sets(d_id) %>% content()
pas_id <- phenotype_association_sets$phenotypeAssociationSets[[1]]$id

## Search for pheotypes in the phenotype association set
phenotypes <- ref_client %>% search_phenotypes(pas_id) %>% content()
phenotypes$phenotypes[[1]]


## End(Not run)

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