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 1.10.1 Index]