taxonInfo: taxonInfo

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

taxonInfo

Description

taxonInfo

Usage

taxonInfo(
  taxon,
  request = NULL,
  ...,
  file = NULL,
  return = TRUE,
  overwrite = FALSE,
  memoised = FALSE
)

Arguments

taxon	can either be Taxon ID, Taxon NCBI ID, or one of its string identifiers: scientific name, common name, abbreviation. It is recommended to use Taxon ID for efficiency. Please note, that not all taxa have all the possible identifiers available. Use the allTaxa function to retrieve the necessary information. For convenience, below is a list of few example taxa: ID Comm.name Scient.name Abbr. NcbiID 1 human Homo sapiens 9606 2 mouse Mus musculus 10090 3 rat Rattus norvegicus 10116 4 salmonid Salmonidae 8015 5 atlantic salmon Salmo salar ssal 8030 6 rainbow trout Oncorhynchus mykiss omyk 8022 7 whitefish Coregonus clupeaformis cclu 59861 8 chinook salmon Oncorhynchus tshawytscha otsh 74940 10 rainbow smelt Osmerus mordax omor 8014 11 yeast Saccharomyces cerevisiae 4932 12 zebrafish Danio rerio 7955 13 fly Drosophila melanogaster 7227 14 worm Caenorhabditis elegans 6239 If a vector of length>1 is provided return all matching taxon objects similar to allTaxa but without access to additional parameters. request parameter cannot be specified for vector inputs
request	character. If NULL retrieves the dataset object. Otherwise datasets: Retrieves datasets for the given taxon. Parameters: filter: Optional see allPlatforms filter argument. 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. sort: Character. Optional parameter (defaults to +id) sets the ordering property and direction. Format is [+,-][property name]. E.g. "-accession" will translate to descending ordering by the Accession property. Note that this does not guarantee the order of the returned entities. Nested properties are also supported (recursively). E.g: +curationDetails.lastTroubledEvent.date phenotypes: Loads all phenotypes for the given taxon. Paremeters: editableOnly: Optional, defaults to FALSE. Whether to only list editable objects. tree: Optional, defaults to FALSE. Whether the returned structure should be an actual tree (nested JSON objects). Default is false - the tree is flattened and the tree structure information is stored as the values of the returned object. phenoCandidateGenes: Given a set of phenotypes, return all genes associated with them. Parameters: editableOnly: Optional, defaults to FALSE. Whether to only list editable objects. phenotypes: Required. Phenotype value URIs separated by commas. gene: Retrieves genes matching the identifier on the given taxon. Parameters: gene: 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). geneEvidence: Retrieves gene evidence for the gene on the given taxon. Parameters: gene: Required. Same as "gene" request geneLocation: Retrieves gene evidence for the gene on the given taxon. Parameters: gene: Required. Same as "gene" request genesAtLocation: Finds genes overlapping a given region. Parameters: chromosome: Required. The chromosome of the query location. Eg: 3, 21, X strand: Optional. Can either be + or -. This is a WIP parameter and does currently not do anything. When using in scripts, remember to URL-encode the '+' plus character (see the compiled URL below). start: Required. Number of the start nucleotide of the desired region. size: Required. Amount of nucleotides in the desired region (i.e. the length of the region). If a vector of length>1 is provided return all matching taxon objects similar to allTaxa request parameter cannot be specified for vector inputs
...	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

taxonInfo('human')
taxonInfo('human', request = 'datasets')
taxonInfo('human',request = 'phenotypes')
taxonInfo('human',request = 'phenoCandidateGenes',
    phenotypes = c('http://purl.obolibrary.org/obo/DOID_11934',
                   'http://purl.obolibrary.org/obo/DOID_3119'))
taxonInfo('human', request= 'gene',gene='DYRK1A')
taxonInfo('human', request= 'geneLocation',gene='DYRK1A')

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