gene_search: Search for Gene Information Based on a Query

In genular: 'Genular' Database API

Search for Gene Information Based on a Query

Description

This function allows users to search for gene information by sending a POST request to the 'Genular' API. It accepts various search parameters and returns information about genes that match the search criteria.

Usage

gene_search(
  queryFields,
  queryValues,
  fieldsFilter = c("geneID", "symbol", "crossReference.enseGeneID"),
  excludeFields = NULL,
  page = 1,
  limit = 10,
  searchType = "and",
  orderBy = "geneID",
  sortDirection = "asc",
  responseType = "json",
  matchType = "exact",
  organismType = list(c("9606")),
  ontologyCategories = list(),
  debug = 0,
  options = list()
)

Arguments

queryFields	A character vector specifying the fields to search within the gene data.
queryValues	A numeric vector representing the values to search for within the specified fields.
fieldsFilter	An optional character vector specifying which fields to include in the response.
excludeFields	If fieldsFilter is not provided (empty), all fields are returned, here you can specify the fields you want to exclude.
page	An integer specifying the page number of the search results to retrieve.
limit	An integer specifying the maximum number of results to return per page.
searchType	A character string indicating whether to use 'and' or 'or' logic for multiple search conditions.
orderBy	A character string specifying which field to sort the results by.
sortDirection	A character string indicating the sort direction ('asc' or 'desc').
responseType	A character string indicating the type of response to expect ('json' or 'csv').
matchType	A character string indicating the type of match to perform ('exact' or 'regex').
organismType	A list of organism type IDs to filter the search results.
ontologyCategories	A list of ontology category IDs to filter the search results.
debug	An integer value indicating whether to enable debug mode (1) or not (0).
options	A list of additional options for the API request, including endpoint, api_key, timeout, and user-agent.

Value

Depending on the responseType parameter, this function returns a list with different elements: If responseType is 'json', the function returns a list containing the HTTP status code ('status_code'), the parsed JSON content ('content') representing gene information matching the search criteria, and the original request body sent to the API ('request_body'). If responseType is 'csv', the function returns a list containing the HTTP status code ('status_code'), a data frame ('content') constructed from the CSV response representing gene information, and the original request body sent to the API ('request_body'). In case of an HTTP status code different from 200, the content part of the return value provides the received error message or data.

Examples

# Define search parameters
queryFields <- list(c("geneID")) # or c("geneID", "symbol" ...)
queryValues <- c(1, 56, 70)
searchType <- "or"
fieldsFilter <- c("geneID", "symbol", "crossReference.enseGeneID")

# Execute the search
gene_search_results <- gene_search(queryFields, queryValues, 
                                     fieldsFilter, searchType = searchType, 
                                     page = 1, limit = 10)

# Print the results
print(gene_search_results)

genular documentation built on Oct. 19, 2024, 9:07 a.m.