geneInfo: geneInfo

In oganm/gemmaAPI: A wrapper for Gemma's restful API

geneInfo

Description

geneInfo

Usage

geneInfo(
  gene,
  request = NULL,
  ...,
  file = NULL,
  return = TRUE,
  overwrite = FALSE,
  memoised = FALSE
)

Arguments

gene	Can either be the NCBI ID (1859), Ensembl ID (ENSG00000157540) or official symbol (DYRK1A) of the gene. NCBI ID is the most efficient (and guaranteed to be unique) identifier. Official symbol represents a gene homologue for a random taxon, unless used in a specific taxon (see the Taxa Endpoints). If a vector of length>1 is provided all matching gene objects will be returned.
request	Character. If NULL retrieves all genes matching the identifier. Otherwise evidence: Retrieves gene evidence for the given gene locations: Retrieves the physical location of the given gene probes: Retrieves the probes (composite sequences) with this gene. Parameters: offset: Optional, defaults to 0. Skips the specified amount of objects when retrieving them from the database. limit: Optional, defaults to 20. Limits the result to specified amount of objects. Use 0 for no limit. goTerms: Retrieves the GO terms of the given gene coexpression: Retrieves the coexpression of two given genes. Parameters: with: Required. Can either be the NCBI ID (1859), Ensembl ID (ENSG00000157540) or official symbol (DYRK1A) of the gene. NCBI ID is the most efficient (and guaranteed to be unique) identifier. Official symbol represents a gene homologue for a random taxon, unless used in a specific taxon (see the Taxa Endpoints). limit: Optional, defaults to 100. Limits the result to specified amount of objects. Use 0 for no limit. stringency: Optional, defaults to 1. Sets the stringency of coexpression search.
...	Use if the specified request has additional parameters.
file	Character. File path. If provided, response will be saved to file
return	Logical. If the response should be returned. Set to false when you only want to save a file
overwrite	Logical. If TRUE, existing files will be overwritten. If FALSE a warning will be thrown and no action is taken.
memoised	Logical. If TRUE a memoised version of the function will be used which is faster for repeated requests. Use forgetGemmaMemoised to clear memory.

Value

A list

Examples

geneInfo(1859)
geneInfo('1859') # single match it is a unique NCBI id
geneInfo('DYRK1A') # this returns all genes named DYRK1A from all species

geneInfo('1859','goTerms')
geneInfo('1859','locations')
geneInfo('1859','probes')
geneInfo('1859','evidence')

oganm/gemmaAPI documentation built on July 23, 2022, 8:26 p.m.