getGlobal {psichomics} | R Documentation

## 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)

    setASevent(event)

    getEvent()

    setEvent(event)

    getGenes()

    getCategories()

    getCategory()

    setCategory(category)

    getCategoryData()

    getActiveDataset()

    setActiveDataset(dataset)

    getClinicalData(attrs = NULL)

    getPatientId()

    getPatientAttributes()

    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())

    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 (e.g. "Carcinoma 2016"); by default, it uses the selected data category
`...` | Arguments to identify a variable
`sep` | Character to separate identifiers
`value` | Value to attribute to an element
`data` | List of data frame or matrix to set as data
`name` | Character: data table name
`auto` | Boolean: enable automatic navigation of browser history?
`integer` | Integer: value of the setting
`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
`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

`getGlobal`, `getClinicalMatchFrom`, `getGroups` and `getDifferentialSplicing`

[Package psichomics version 1.8.2 Index]