getGlobal: Get or set globally accessible elements

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Get or set globally accessible elements

Description

Get or set globally accessible elements

Usage

getGlobal(category = getCategory(), ..., sep = "_")

setGlobal(category = getCategory(), ..., value, sep = "_")

setData(data)

setDataTable(name, value, category = getCategory())

getAutoNavigation()

setAutoNavigation(auto)

getCores()

setCores(integer)

getSignificant()

setSignificant(integer)

getPrecision()

setPrecision(integer)

getASevents()

getAnnotationHub()

setAnnotationHub(ah)

getASevent()

setASevent(event, data = NULL)

getEvent()

setEvent(event, data = NULL)

getGenes()

getCategories()

getCategory()

setCategory(category)

getCategoryData()

getActiveDataset()

setActiveDataset(dataset)

getClinicalData(attrs = NULL)

getSubjectId()

getSubjectAttributes()

getSampleInfo()

setSampleInfo(value, category = getCategory())

getSampleId()

getSampleAttributes()

getJunctionQuantification(category = getCategory())

getGeneExpression(item = NULL, category = getCategory(), EList = FALSE)

setNormalisedGeneExpression(geneExpr, category = getCategory())

getInclusionLevels()

setInclusionLevels(incLevels, category = getCategory())

getInclusionLevelsSummaryStatsCache(category = getCategory())

setInclusionLevelsSummaryStatsCache(cache, category = getCategory())

getPCA(category = getCategory())

setPCA(pca, category = getCategory())

getICA(category = getCategory())

setICA(ica, category = getCategory())

getCorrelation(category = getCategory())

setCorrelation(correlation, category = getCategory())

getGroupIndependenceTesting(category = getCategory())

setGroupIndependenceTesting(groupIndependenceTesting, category = getCategory())

getSpecies(category = getCategory())

setSpecies(species, category = getCategory())

getAssemblyVersion(category = getCategory())

setAssemblyVersion(assembly, category = getCategory())

getAnnotationName(category = getCategory())

setAnnotationName(annotName, category = getCategory())

getURLtoDownload()

setURLtoDownload(url)

Arguments

category	Character: data category
...	Arguments to identify a variable
sep	Character to separate identifiers
value	Value to attribute to an element
data	Matrix or data frame: alternative splicing information
name	Character: data table name
auto	Boolean: enable automatic navigation of browser history?
integer	Integer: value of the setting
ah	AnnotationHub
event	Character: alternative splicing event
dataset	Character: dataset name
attrs	Character: name of attributes to retrieve (if NULL, the whole dataset is returned)
item	Character: name of specific item to retrieve (if NULL, the whole list is returned)
EList	Boolean: return gene expression datasets as EList if possible or as data frames?
geneExpr	Data frame or matrix: normalised gene expression
incLevels	Data frame or matrix: inclusion levels
cache	List of summary statistics
pca	prcomp object (principal component analysis)
ica	Object containing independent component analysis
correlation	prcomp object (correlation analyses)
groupIndependenceTesting	Object containing group independence testing results
species	Character: species
assembly	Character: assembly version
annotName	Character: annotation name
url	Character: URL links to download

Value

Getters return globally accessible data, whereas setters return NULL as they are only used to modify the Shiny session's state

Note

Needs to be called inside a reactive function

See Also

Other functions to get and set global variables: getClinicalMatchFrom(), getDifferentialExpression(), getDifferentialSplicing(), getGroups(), getHighlightedPoints(), getSelectedDataPanel()

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.