new.scoreSet: New R-API MaveDB ScoreSet

In jweile/rapimave: R API for MaveDB

Description

Internal constructor that creates an immutable new ScoreSet object. This function is not exported and should not be called outside of the rapimave package itself. ScoreSet objects are generated by the getAllScoreSets() and getScoreSet() methods of a rapimave object (which itself is generated using the new.rapimave() constructor). However, this section explains the functions that are available for these objects.

Usage

new.scoreSet(data)

Details

A ScoreSet object offers the following getter functions:

• getContributors() returns a list of users that contributed to this ScoreSet.

• getURN() returns the URN of this ScoreSet.

• getCreationDate() returns the date when this record was originally created.

• getModificationDate() returns the date when this record was last modified.

• getPublicationDate() returns the date when this record was published.

• getCreatedBy() returns the user who originally created this record.

• getModifiedBy() returns the user who last modified this record.

• getMetadata() returns the metadata for this record.

• getTitle() returns the title of this record.

• getShortDescription() returns a short description text of this record.

• getAbstract() returns the abstract text of this record.

• getMethods() returns the methods description text of this record.

• getKeywords() returns the list of keywords associated with this record.

• getDOIs() returns the list of Digital Object Identifiers (DOIs) associated with this record.

• getXRefPubmed() returns cross-references to Pubmed.

• getTarget() returns the Target object for this scoreset, which describes the molecule that that was targeted in the experiment.

• getLicence() returns the licencing information governing the use of this ScoreSet.

• getCurrentVersion() If a more up-to-date version of this ScoreSet exists, that has since replaced it, this function will return the accession of the most recent version.

• getPreviousVersion() If this ScoreSet replaces an older ScoreSet, this function returns the accession of that older ScoreSet.

• getNextVersion() If this ScoreSet was replaced by newer ScoreSet, this function returns the accession of that newer ScoreSet in versioning history. To obtain the most recent version, use getCurrentVersion().

• getCountColumns() returns the column names in the count table for this ScoreSet.

• getScoreColumns() returns the column names in the score table for this ScoreSet.

• getVariantCount() returns the number of variants in this scoreset, i.e. the number of rows to be expected in the scores and counts tables.

• getExperiment() returns the URN of the experiment record to which this scoreset belongs.

• isMetaAnalysis() returns whether this dataset represents a meta-analysis of existing data.

• getDataUsagePolicy() returns any data usage policy text for this ScoreSet.

Value

a new R-API MaveDB ScoreSet object.

Examples

## Not run: 
mave <- new.rapimave()
set1 <- mave$getScoreSet("urn:mavedb:00000001-a-1")
scoreColNames <- set1$getScoreColumns()

## End(Not run)

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