Description Usage Arguments Details Value Examples
Creates an object of type rapimave.
1 2 3 4 5 | new.rapimave(
baseURL = "https://www.mavedb.org/api/",
certifySSL = FALSE,
encoding = "UTF-8"
)
|
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 |
encoding |
A string specifying the expected character encoding used by the webservice. Defaults to "UTF-8" |
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.
MaveDB R-API object with functions accessbile via the $ operator.
1 2 3 4 | ## Not run:
mave <- new.rapimave()
## End(Not run)
|
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