new.rapimave: MaveDB R-API client constructor

In jweile/rapimave: R API for MaveDB

Description

Creates an object of type rapimave.

Usage

new.rapimave(
  baseURL = "https://www.mavedb.org/api/",
  certifySSL = FALSE,
  encoding = "UTF-8"
)

Arguments

baseURL	MaveDB API base-URL. Defaults to "https://www.mavedb.org/api/"
certifySSL	Logical indicating whether to certify SSL certificates when querying the database. Defaults to FALSE.
encoding	A string specifying the expected character encoding used by the webservice. Defaults to "UTF-8"

Details

The resulting object offers the following functions:

• getAllUsers() returns a list of all user objects. See new.user for available methods on user objects.

• getUser(username) returns the user object for the given username. Usernames are usually ORCID IDs. See https://orcid.org/ for information on ORCID. See new.user for available methods on user objects.

• findExperimentSets(filter) returns a list of all ExperimentSet objects that match the given filter word. See new.experimentSet for available methods on ExperimentSet objects.

• getAllExperimentSets() returns a list of all ExperimentSet objects. See new.experimentSet for available methods on ExperimentSet objects.

• getExperimentSet(urn) returns the ExperimentSet object for the given URN. ExperimentSet URNs usually follow the syntax /^urn:mavedb:\d+$/ . See new.experimentSet for available methods on ExperimentSet objects.

• getAllExperiments() returns a list of all Experiment objects. See new.experiment for available methods on Experiment objects.

• findExperiments(filter) returns a list of all Experiment objects that match the given filter word. See new.experiment for available methods on Experiment objects.

• getExperiment(urn) returns the Experiment object for the given URN. Experiment URNs usually follow the syntax /^urn:mavedb:\d+-\w+/ . See new.experiment for available methods on Experiment objects.

• getAllScoreSets() returns a list of all ScoreSet objects. See new.scoreSet for available methods on ScoreSet objects.

• findScoreSets(filter) returns a list of all ScoreSet objects that match the given filter word. See new.scoreSet for available methods on ScoreSet objects.

• getScoreSet(urn) returns the ScoreSet object for the given URN. ScoreSet URNs usually follow the syntax /^urn:mavedb:\d+-\w+-\d+$/ . See new.scoreSet for available methods on ScoreSet objects.

• getScores(urn) returns a data.frame with the scores for the given ScoreSet URN

• getCounts(urn) returns a data.frame with the counts for the given ScoreSet URN

• getMetadata(urn) returns a data.frame with the metadata for the given ScoreSet URN

• getKeywords() returns all currently used keywords across MaveDB.

• getAllPubmed() returns all currently used Pubmed IDs across MaveDB.

• getAllDOI() returns all currently used DOIs across MaveDB.

• getAllSRA() returns all currently used SRA IDs across MaveDB.

• getAllRefseq() returns all currently used Refseq IDs across MaveDB.

• getAllUniprot() returns all currently used Uniprot IDs across MaveDB.

• getAllEnsembl() returns all currently used Ensembl IDs across MaveDB.

• getAllAssemblies() returns all currently used Genome assemblies across MaveDB.

• getAllTargets() returns all currently used target sequences across MaveDB.

• getReferenceGenomes() returns all currently used reference genomes across MaveDB.

Value

MaveDB R-API object with functions accessbile via the $ operator.

Examples

## Not run: 
mave <- new.rapimave()

## End(Not run)

jweile/rapimave documentation built on Aug. 4, 2021, 12:12 a.m.