# Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

## Documentation for package ‘psichomics’ version 1.6.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U V W

## -- A --

addObjectAttrs | Set attributes to an object
addTCGAdata | Creates a UI set with options to add data from TCGA/Firebrowse
analysesPlotSet | Set of functions to plot differential analyses
analysesServer | Server logic
analysesTableSet | Set of functions to render data table for differential analyses
analysesUI | User interface
appendNewGroups | Append new groups to already existing groups
appServer | Server logic
appUI | User interface
areSplicingEvents | Check if string identifies splicing events
articleUI | Return the interface to display an article
ASquantFileInput | File input for alternative splicing quantification
assignColours | Assign colours to groups
assignValuePerPatient | Assign average sample values to their corresponding patients
assignValuePerSubject | Assign average sample values to their corresponding patients

## -- B --

basicStats | Basic statistics performed on data
blendColours | Blend two HEX colours
browserHistory | Enable history navigation
bsModal2 | Modified version of 'shinyBS::bsModal'

## -- C --

calculateInclusionLevels | Calculate inclusion levels using alternative splicing event annotation and junction quantification for many samples
calculateLoadingsContribution | Calculate the contribution of PCA loadings to the selected principal components
checkFileFormat | Checks the format of a file
checkFirebrowse | Return an user interface depending on the status of the Firebrowse API
checkIntegrity | Compute the 32-byte 'MD5' hashes of one or more files and check with given 'md5' file
checkSurvivalInput | Prepare survival terms in case of valid input
closeProgress | Close the progress even if there's an error
clusterICAset | Server logic for clustering ICA data
clusterSet | Server logic for clustering PCA data
colourInputMod | Modified colour input with 100% width
correlateGEandAS | Correlate gene expression data against alternative splicing quantification
correlationServer | Server logic
correlationUI | User interface
createDataTab | Render a specific data tab (including data table and related interface)
createDensitySparklines | Create density sparklines for inclusion levels
createEventPlotting | Create plot for events
createGroup | Prepare to create group according to specific details
createGroupByAttribute | Split elements into groups based on a given column of a dataset
createGroupByColumn | Split elements into groups based on a given column of a dataset
createGroupById | Create groups based on given row indexes or identifiers
createGroupFromInput | Set new groups according to the user input
createJunctionsTemplate | Creates a template of alternative splicing junctions
createOptimalSurvData | Create survival data based on a PSI cutoff
createSparklines | Create sparkline charts to be used in a data table

## -- D --

dataServer | Server logic
dataUI | User interface
diffAnalyses | Perform statistical analyses
diffAnalysis | Perform statistical analyses
diffExpressionEventServer | Server logic
diffExpressionEventUI | User interface
diffExpressionServer | Server logic
diffExpressionSet | Set of functions to perform differential analyses
diffExpressionTableServer | Server logic
diffExpressionTableUI | User interface
diffExpressionUI | User interface
diffSplicingEventServer | Server logic
diffSplicingEventUI | User interface
diffSplicingServer | Server logic
diffSplicingSet | Set of functions to perform differential analyses
diffSplicingTableServer | Server logic
diffSplicingTableUI | User interface
diffSplicingUI | User interface
dimReductionServer | Server logic
dimReductionUI | User interface
disableTab | Enable or disable a tab from the 'navbar'
display | Display characters in the command-line
downloadFiles | Download files to a given directory

## -- E --

enableTab | Enable or disable a tab from the 'navbar'
endProcess | Signal the program that a process has ended
ensemblToUniprot | Convert an Ensembl identifier to the respective UniProt identifier
errorAlert | Show or remove an alert
errorDialog | Alert in the style of a dialogue box with a button
errorModal | Style and show a modal
escape | Escape symbols for use in regular expressions
eventPlotOptions | Options for event plotting
export_highcharts | Add an exporting feature to a 'highcharts' object

## -- F --

fileBrowser | Interactive folder selection using a native dialogue
fileBrowserInput | File browser input
filterGroups | Filter groups with less data points than the threshold
findASeventsFromGene | Find splicing events based on given genes
firebrowseServer | Server logic
firebrowseUI | User interface
fisher | Perform Fisher's exact test and return interface to show the results
fligner | Perform Fligner-Killeen test and return interface to show the results

## -- G --

geneExprFileInput | File input for gene expression
geneExprSurvSet | Logic set to perform survival analysis based on gene expression cut-offs
geNormalisationFilteringInterface | Interface to normalise and filter gene expression
geNormalisationFilteringServer | Server logic
geNormalisationFilteringUI | User interface
getActiveDataset | Get or set globally accessible elements
getAnnotationName | Get or set globally accessible elements
getASevent | Get or set globally accessible elements
getASevents | Get or set globally accessible elements
getAssemblyVersion | Get or set globally accessible elements
getAttributesTime | Retrieve the time for given columns in a clinical dataset
getAutoNavigation | Get or set globally accessible elements
getCategories | Get or set globally accessible elements
getCategory | Get or set globally accessible elements
getCategoryData | Get or set globally accessible elements
getClinicalData | Get or set globally accessible elements
getClinicalDataForSurvival | Retrieve clinical data based on attributes required for survival analysis
getClinicalMatchFrom | Get or set clinical matches from a given data type
getColumnsTime | Retrieve the time for given columns in a clinical dataset
getCores | Get or set globally accessible elements
getCorrelation | Get or set globally accessible elements
getData | Get global data
getDataRows | Get rows of a data frame between two row indexes
getDifferentialExpression | Get or set differential expression' elements for a data category
getDifferentialExpressionColumns | Get or set differential expression' elements for a data category
getDifferentialExpressionFiltered | Get or set differential expression' elements for a data category
getDifferentialExpressionResetPaging | Get or set differential expression' elements for a data category
getDifferentialExpressionSurvival | Get or set differential expression' elements for a data category
getDifferentialSplicing | Get or set differential splicing' elements for a data category
getDifferentialSplicingColumns | Get or set differential splicing' elements for a data category
getDifferentialSplicingFiltered | Get or set differential splicing' elements for a data category
getDifferentialSplicingResetPaging | Get or set differential splicing' elements for a data category
getDifferentialSplicingSurvival | Get or set differential splicing' elements for a data category
getDownloadsFolder | Get the Downloads folder of the user
getEvent | Get or set globally accessible elements
getFirebrowseCohorts | Query the Firebrowse web API for available cohorts
getFirebrowseDataTypes | Get data types available from Firebrowse
getFirebrowseDateFormat | Returns the date format used by the Firebrowse web API
getFirebrowseDates | Query the Firebrowse web API for the available data datestamps
getFirehoseCohorts | Query the Firebrowse web API for available cohorts
getFirehoseDataTypes | Get data types available from Firebrowse
getFirehoseDates | Query the Firebrowse web API for the available data datestamps
getGeneExpression | Get or set globally accessible elements
getGenes | Get or set globally accessible elements
getGenesFromSplicingEvents | Retrieve genes based on given alternative splicing events
getGlobal | Get or set globally accessible elements
getGroupIndependenceTesting | Get or set globally accessible elements
getGroups | Get or set groups
getGTExTissues | Get GTEx tissues from given GTEx sample attributes
getGtexTissues | Get GTEx tissues from given GTEx sample attributes
getHidden | Get or set hidden globally accessible elements
getHighlightedPoints | Get or set points or regions for plots
getICA | Get or set globally accessible elements
getInclusionLevels | Get or set globally accessible elements
getJunctionQuantification | Get or set globally accessible elements
getLabelledPoints | Get or set points or regions for plots
getMatchingSamples | Get samples matching the given patients
getNumerics | Convert a column to numeric if possible and ignore given columns composed of lists
getPatientAttributes | Get or set globally accessible elements
getPatientFromSample | Get patients from given samples
getPatientId | Get or set globally accessible elements
getPCA | Get or set globally accessible elements
getPrecision | Get or set globally accessible elements
getPSIperPatient | Assign average sample values to their corresponding patients
getSampleAttributes | Get or set globally accessible elements
getSampleFromPatient | Get samples matching the given patients
getSampleFromSubject | Get samples matching the given patients
getSampleId | Get or set globally accessible elements
getSampleInfo | Get or set globally accessible elements
getSelectedGroups | Group selection
getSelectedPoints | Get or set points or regions for plots
getServerFunctions | Matches server functions from a given loader
getSignificant | Get or set globally accessible elements
getSpecies | Get or set globally accessible elements
getSplicingEventCoordinates | Returns the coordinates of interest for a given event type
getSplicingEventFromGenes | Retrieve alternative splicing events based on given genes
getSplicingEventTypes | Splicing event types available
getSubjectFromSample | Get patients from given samples
getTCGAcohorts | Query the Firebrowse web API for available cohorts
getTCGAdates | Query the Firebrowse web API for the available data datestamps
getUiFunctions | Matches user interface (UI) functions from a given loader
getURLtoDownload | Get or set globally accessible elements
getValidEvents | Filters the events with valid elements according to the given validator
getValuePerPatient | Assign average sample values to their corresponding patients
getValuePerSubject | Assign average sample values to their corresponding patients
getZoom | Get or set points or regions for plots
ggplotAuxServer | Logic set to create an interactive ggplot
ggplotServer | Logic set to create an interactive ggplot
ggplotTooltip | Create the interface for the tooltip of a plot
ggplotUI | Interface for interactive ggplot
globalSelectize | Create a selectize input available from any page
groupByAttribute | User interface to group by attribute
groupByExpression | User interface to group by subset expression
groupByGrep | User interface to group by grep expression
groupById | User interface to group by row
groupManipulation | Logic server to manipulate data grouping
groupManipulationInput | Interface to manipulate data grouping
groupPerElem | Assign one group to each element
groupPerPatient | Assign one group to each element
groupPerSample | Assign one group to each element
groupsServer | Server logic
groupsServerOnce | Server function for data grouping (one call)
groupsUI | User interface
gtexDataServer | Server logic
gtexDataUI | User interface

## -- H --

hchart.survfit | Plot survival curves using Highcharts
hc_scatter | Create scatter plot
helpServer | Server logic
helpUI | User interface

## -- I --

icaServer | Server logic
icaUI | User interface
inclusionLevelsInterface | Interface to quantify alternative splicing
inclusionLevelsServer | Server logic
inclusionLevelsUI | User interface
infoModal | Style and show a modal
infoServer | Server logic
infoUI | User interface
inlineDialog | Alert in the style of a dialogue box with a button
insideFile | Get psichomics file inside a given directory
is.whole | Check if a number is whole
isFile | Check if files exist
isFirebrowseUp | Check whether the Firebrowse web API is running
isFirehoseUp | Check whether the Firebrowse web API is running
isRStudioServer | Check if running in RStudio Server

## -- J --

joinEventsPerType | Full outer join all given events based on select columns
junctionString | String used to search for matches in a junction quantification file

## -- K --

kruskal | Perform Kruskal's test and return interface to show the results

## -- L --

labelBasedOnCutoff | Label groups based on a given cutoff
levene | Perform Levene's test and return interface to show the results
leveneTest | Levene's test
linkToArticle | Interface that directs users to original article
linkToRunJS | Link to run arbitrary JavaScript code
listAllAnnotations | List alternative splicing annotation files available, as well as custom annotation
listSplicingAnnotations | List the alternative splicing annotation files available
loadAnnotation | Load alternative splicing annotation from 'AnnotationHub'
loadBy | Check if a given function should be loaded by the calling module
loadCustomSplicingAnnotationSet | Set of functions to load a custom alternative splicing annotation
loadedDataModal | Create a modal warning the user of already loaded data
loadFile | Loads a file according to its format
loadFileFormats | Loads file formats
loadFirebrowseData | Downloads and processes data from the Firebrowse web API and loads it into R
loadFirebrowseFolders | Load Firebrowse folders
loadFirehoseData | Downloads and processes data from the Firebrowse web API and loads it into R
loadFirehoseFolders | Load Firebrowse folders
loadGeneExpressionSet | Set of functions to load splicing quantification
loadGtexData | Load GTEx data
loadGtexDataShiny | Shiny wrapper to load GTEx data
loadGTExFile | Load GTEx file
loadGtexFile | Load GTEx file
loadLocalFiles | Load local files
loadRequiredData | Missing information modal template
loadSplicingQuantificationSet | Set of functions to load splicing quantification
loadSRAproject | Download and load SRA projects
loadTCGAdata | Downloads and processes data from the Firebrowse web API and loads it into R
loadTCGAfolders | Load Firebrowse folders
loadTCGAsampleMetadata | Prepare TCGA sample metadata from loaded datasets
localDataServer | Server logic
localDataUI | User interface

## -- M --

matchGroupPatientsAndSamples | Match patients and samples in a group
matchSplicingEventsWithGenes | Match splicing events with respective genes
missingDataGuide | Missing information modal template
missingDataModal | Missing information modal template
modTabPanel | Modified 'tabPanel' function to show icon and title

## -- N --

navSelectize | Create a special selectize input in the navigation bar
noinfo | Interface when no information could be retrieved
normaliseGeneExpression | Filter and normalise gene expression

## -- O --

operateOnGroups | Set operations on groups
optimalPSIcutoff | Calculate optimal data cutoff that best separates survival curves
optimalSurvivalCutoff | Calculate optimal data cutoff that best separates survival curves
optimSurvDiffSet | Optimal survival difference given an inclusion level cutoff for a specific alternative splicing event

## -- P --

parseCategoricalGroups | Parse categorical columns in a data frame
parseDateResponse | Parse the date from a response
parseFirebrowseMetadata | Query the Firebrowse web API for metadata
parseFirehoseMetadata | Query the Firebrowse web API for metadata
parseMatsA3SS | Parse junctions of an alternative splicing event from MATS according to event type
parseMatsA5SS | Parse junctions of an alternative splicing event from MATS according to event type
parseMatsAFE | Parse junctions of an alternative splicing event from MATS according to event type
parseMatsALE | Parse junctions of an alternative splicing event from MATS according to event type
parseMatsAnnotation | Get events from alternative splicing annotation
parseMatsEvent | Parse alternative splicing events from MATS
parseMatsGeneric | Parse junctions of an alternative splicing event from MATS according to event type
parseMatsMXE | Parse junctions of an alternative splicing event from MATS according to event type
parseMatsRI | Parse junctions of an alternative splicing event from MATS according to event type
parseMatsSE | Parse junctions of an alternative splicing event from MATS according to event type
parseMisoA3SS | Parse junctions of an event from MISO according to event type
parseMisoA5SS | Parse junctions of an event from MISO according to event type
parseMisoAFE | Parse junctions of an event from MISO according to event type
parseMisoALE | Parse junctions of an event from MISO according to event type
parseMisoAnnotation | Get events from alternative splicing annotation
parseMisoEvent | Parse an alternative splicing event from MISO
parseMisoEventID | Match MISO's splicing event IDs with the IDs present in the alternative splicing annotation file and get events in a data frame
parseMisoGeneric | Parse junctions of an event from MISO according to event type
parseMisoId | Parse MISO's alternative splicing event identifier
parseMisoMXE | Parse junctions of an event from MISO according to event type
parseMisoRI | Parse junctions of an event from MISO according to event type
parseMisoSE | Parse junctions of an event from MISO according to event type
parseMisoTandemUTR | Parse junctions of an event from MISO according to event type
parseSampleGroups | Return the type of a given sample
parseSplicingEvent | Parse an alternative splicing event based on a given identifier
parseSuppaA3SS | Parse junctions of an event from SUPPA
parseSuppaA5SS | Parse junctions of an event from SUPPA
parseSuppaAFE | Parse junctions of an event from SUPPA
parseSuppaALE | Parse junctions of an event from SUPPA
parseSuppaAnnotation | Get events from alternative splicing annotation
parseSuppaEvent | Parses splicing events of a specific event type from SUPPA
parseSuppaGeneric | Parse junctions of an event from SUPPA
parseSuppaMXE | Parse junctions of an event from SUPPA
parseSuppaRI | Parse junctions of an event from SUPPA
parseSuppaSE | Parse junctions of an event from SUPPA
parseTCGAmetadata | Query the Firebrowse web API for metadata
parseTCGAsampleInfo | Parse sample information from TCGA samples
parseTcgaSampleInfo | Parse sample information from TCGA samples
parseUniprotXML | Parse XML from UniProt's RESTful service
parseUrlsFromFirebrowseResponse | Retrieve URLs from a response to a Firebrowse data query
parseUrlsFromFirehoseResponse | Retrieve URLs from a response to a Firebrowse data query
parseValidFile | Parse file given a list of file formats
parseVastToolsA3SS | Parse junctions of an event from VAST-TOOLS according to event type
parseVastToolsA5SS | Parse junctions of an event from VAST-TOOLS according to event type
parseVastToolsAnnotation | Get events from alternative splicing annotation
parseVastToolsEvent | Parses an alternative splicing event from VAST-TOOLS
parseVastToolsRI | Parse junctions of an event from VAST-TOOLS according to event type
parseVastToolsSE | Parse junctions of an event from VAST-TOOLS according to event type
patientMultiMatchWarning | Helper text to explain what happens when a patient matches multiple samples when performing survival analysis
pcaServer | Server logic
pcaUI | User interface
performICA | Perform independent component analysis after processing missing values
performPCA | Perform principal component analysis after processing missing values
plot.GEandAScorrelation | Plot correlations
plotClusters | Add clusters to 'highchart' object
plotCorrelation | Plot correlations
plotDensity | Plot distribution through a density plot
plotDistribution | Plot distribution through a density plot
plotGroupIndependence | Plot -log10(p-values) of the results obtained after multiple group independence testing
plotICA | Create multiple scatterplots from ICA
plotPCA | Create a scatterplot from a PCA object
plotPointsStyle | Interface to modify the style of the plot points
plotProtein | Plot protein features
plotSingleICA | Create a scatterplot for ICA
plotSurvivalCurves | Plot survival curves
plottableXranges | HTML code to plot a X-ranges series
plotTranscripts | Plot transcripts
plotVariance | Create the explained variance plot
prepareAnnotationFromEvents | Prepare annotation from alternative splicing events
prepareEventPlotOptions | Prepare event plot options
prepareFileBrowser | Prepare file browser dialogue and update the input's value accordingly to selected file or directory
prepareFirebrowseArchives | Prepares Firebrowse archives in a given directory
prepareFirehoseArchives | Prepares Firebrowse archives in a given directory
prepareGeneQuant | Prepare files to be loaded into psichomics
prepareGeneQuantSTAR | Prepare files to be loaded into psichomics
prepareJunctionQuant | Prepare files to be loaded into psichomics
prepareJunctionQuantSTAR | Prepare files to be loaded into psichomics
prepareSRAmetadata | Prepare files to be loaded into psichomics
prepareTCGAarchives | Prepares Firebrowse archives in a given directory
prepareWordBreak | Create word break opportunities (for HTML) using given characters
processButton | Style button used to initiate a process
processDatasetNames | Process dataset names
processSurvData | Process survival data to calculate survival curves
processSurvival | Check if survival analyses successfully completed or returned errors
processSurvTerms | Process survival curves terms to calculate survival curves
psichomics | Start graphical interface of psichomics
pubmedUI | Return the interface of relevant PubMed articles for a given gene

## -- Q --

quantifySplicing | Quantify alternative splicing events
quantifySplicingSet | Set of functions to quantify alternative splicing
queryEnsembl | Query the Ensembl REST API
queryEnsemblByEvent | Query information from Ensembl by a given alternative splicing event
queryEnsemblByGene | Query information from Ensembl by a given gene
queryFirebrowseData | Query the Firebrowse web API for TCGA data
queryFirehoseData | Query the Firebrowse web API for TCGA data
queryPubMed | Query the PubMed REST API
queryUniprot | Query the UniProt REST API

## -- R --

readAnnot | Read custom or remote annotation
readFile | Load local file
recountDataServer | Server logic
recountDataUI | User interface
reduceDimensionality | Reduce dimensionality after processing missing values from data frame
removeAlert | Show or remove an alert
renameDuplicated | Rename vector to avoid duplicated values with another vector
renameGroups | Rename duplicated names from a new group
renderDataTableSparklines | Render a data table with sparkline HTML elements
renderGeneticInfo | Render genetic information
renderGroupInterface | Render group interface
renderProteinInfo | Render protein information
rm.null | Filter NULL elements from vector or list
roundDigits | Round by the given number of digits
roundMaxUp | Round down/up the minimum/maximum value
roundMinDown | Round down/up the minimum/maximum value
rowMeans | Calculate mean for each row of a matrix
rowVars | Calculate variance for each row of a matrix

## -- S --

selectGroupsServer | Group selection
selectGroupsUI | Group selection
selectizeGeneInput | Create input to select a gene
setActiveDataset | Get or set globally accessible elements
setAnnotationName | Get or set globally accessible elements
setASevent | Get or set globally accessible elements
setAssemblyVersion | Get or set globally accessible elements
setAutoNavigation | Get or set globally accessible elements
setCategory | Get or set globally accessible elements
setClinicalMatchFrom | Get or set clinical matches from a given data type
setCores | Get or set globally accessible elements
setCorrelation | Get or set globally accessible elements
setData | Get or set globally accessible elements
setDataTable | Get or set globally accessible elements
setDifferentialExpression | Get or set differential expression' elements for a data category
setDifferentialExpressionColumns | Get or set differential expression' elements for a data category
setDifferentialExpressionFiltered | Get or set differential expression' elements for a data category
setDifferentialExpressionResetPaging | Get or set differential expression' elements for a data category
setDifferentialExpressionSurvival | Get or set differential expression' elements for a data category
setDifferentialSplicing | Get or set differential splicing' elements for a data category
setDifferentialSplicingColumns | Get or set differential splicing' elements for a data category
setDifferentialSplicingFiltered | Get or set differential splicing' elements for a data category
setDifferentialSplicingResetPaging | Get or set differential splicing' elements for a data category
setDifferentialSplicingSurvival | Get or set differential splicing' elements for a data category
setEvent | Get or set globally accessible elements
setFirebrowseData | Set data from Firebrowse
setGlobal | Get or set globally accessible elements
setGroupIndependenceTesting | Get or set globally accessible elements
setGroups | Get or set groups
setHidden | Get or set hidden globally accessible elements
setHighlightedPoints | Get or set points or regions for plots
setICA | Get or set globally accessible elements
setInclusionLevels | Get or set globally accessible elements
setLabelledPoints | Get or set points or regions for plots
setLocalData | Load local files
setMultipleFilesData | Load local files
setNormalisedGeneExpression | Get or set globally accessible elements
setOperation | Perform set operations on selected groups
setOperationIcon | Create an icon based on set operations
setPCA | Get or set globally accessible elements
setPrecision | Get or set globally accessible elements
setSampleInfo | Get or set globally accessible elements
setSelectedPoints | Get or set points or regions for plots
setSignificant | Get or set globally accessible elements
setSpecies | Get or set globally accessible elements
setURLtoDownload | Get or set globally accessible elements
setZoom | Get or set points or regions for plots
showAlert | Show or remove an alert
showGroupsTable | Present groups table
sidebar | Sidebar without a well
signifDigits | Get number of significant digits
singleDiffAnalyses | Perform statistical analysis on a given splicing event
sortCoordinates | Sort coordinates for some event types
spearman | Perform Spearman's test and return interface to show the results
startProcess | Signal the program that a process is starting
startProgress | Create a progress object
styleModal | Style and show a modal
subsetGeneExpressionFromMatchingGenes | Subset gene expression based on (full or partial) matching genes
survdiff.survTerms | Test differences between survival curves
survfit.survTerms | Compute estimates of survival curves
survivalServer | Server logic
survivalUI | User interface

## -- T --

tabDataset | Creates a 'tabPanel' template for a 'datatable' with a title and description
table2html | Create HTML table from data frame or matrix
tableRow | Create a row for a HTML table
templateServer | Server logic
templateUI | User interface
testGroupIndependence | Multiple independence tests between reference groups and list of groups
testSingleIndependence | Multiple independence tests between a reference group and list of groups
testSurvival | Test the survival difference between groups of patients
testSurvivalCutoff | Test the survival difference between two survival groups given a cutoff
textSuggestions | Create script for auto-completion of text input
toJSarray | Convert vector of values to JavaScript array
transformData | Transform data in data frame
transformOptions | Show variable transformation(s)
transformValues | Transform values as per a given type of transformation
trimWhitespace | Trims whitespace from a word
ttest | Perform unpaired t-test analysis and return interface to show the results

## -- U --

uniqueBy | Check unique rows of a data frame based on a set of its columns
updateClinicalParams | Update available clinical attributes when the clinical data changes
updateFileBrowserInput | Change the value of a fileBrowserInput on the client
updateProgress | Update a progress object

## -- V --

vennEvents | Compare the number of events from the different programs in a Venn diagram

## -- W --

warningAlert | Show or remove an alert
warningDialog | Alert in the style of a dialogue box with a button
warningModal | Style and show a modal
wilcox | Perform Wilcoxon analysis and return interface to show the results