Man pages for psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

addObjectAttrsSet attributes to an object
addTCGAdataCreates a UI set with options to add data from...
analysesPlotSetSet of functions to plot differential analyses
analysesTableSetSet of functions to render data table for differential...
appendNewGroupsAppend new groups to already existing groups
appServerServer logic
appUIUser interface
areSplicingEventsCheck if string identifies splicing events
articleUIReturn the interface to display an article
ASquantFileInputFile input for alternative splicing quantification
assignColoursAssign colours to groups
basicStatsBasic statistics performed on data
blendColoursBlend two HEX colours
browserHistoryEnable history navigation
bsModal2Modified version of 'shinyBS::bsModal'
calculateInclusionLevelsCalculate inclusion levels using alternative splicing event...
calculateLoadingsContributionCalculate the contribution of PCA loadings to the selected...
checkFileFormatChecks the format of a file
checkFirebrowseReturn an user interface depending on the status of the...
checkIntegrityCompute the 32-byte 'MD5' hashes of one or more files and...
checkSurvivalInputPrepare survival terms in case of valid input
closeProgressClose the progress even if there's an error
clusterICAsetServer logic for clustering ICA data
clusterSetServer logic for clustering PCA data
colourInputModModified colour input with 100% width
correlateGEandASCorrelate gene expression data against alternative splicing...
createDataTabRender a specific data tab (including data table and related...
createDensitySparklinesCreate density sparklines for inclusion levels
createEventPlottingCreate plot for events
createGroupPrepare to create group according to specific details
createGroupByAttributeSplit elements into groups based on a given column of a...
createGroupByIdCreate groups based on given row indexes or identifiers
createGroupFromInputSet new groups according to the user input
createJunctionsTemplateCreates a template of alternative splicing junctions
createOptimalSurvDataCreate survival data based on a PSI cutoff
createSparklinesCreate sparkline charts to be used in a data table
diffAnalysesPerform statistical analyses
diffExpressionSetSet of functions to perform differential analyses
diffSplicingSetSet of functions to perform differential analyses
disableTabEnable or disable a tab from the 'navbar'
displayDisplay characters in the command-line
downloadFilesDownload files to a given directory
endProcessSignal the program that a process has ended
ensemblToUniprotConvert an Ensembl identifier to the respective UniProt...
escapeEscape symbols for use in regular expressions
eventPlotOptionsOptions for event plotting
export_highchartsAdd an exporting feature to a 'highcharts' object
fileBrowserInteractive folder selection using a native dialogue
fileBrowserInputFile browser input
filterGroupsFilter groups with less data points than the threshold
findASeventsFromGeneFind splicing events based on given genes
fisherPerform Fisher's exact test and return interface to show the...
flignerPerform Fligner-Killeen test and return interface to show the...
geneExprFileInputFile input for gene expression
geneExprSurvSetLogic set to perform survival analysis based on gene...
geNormalisationFilteringInterfaceInterface to normalise and filter gene expression
getASeventGet or set globally accessible elements
getASeventsGet or set globally accessible elements
getAttributesTimeRetrieve the time for given columns in a clinical dataset
getClinicalDataForSurvivalRetrieve clinical data based on attributes required for...
getClinicalMatchFromGet or set clinical matches from a given data type
getDataGet global data
getDataRowsGet rows of a data frame between two row indexes
getDifferentialExpressionGet or set differential expression' elements for a data...
getDifferentialSplicingGet or set differential splicing' elements for a data...
getDownloadsFolderGet the Downloads folder of the user
getEventGet or set globally accessible elements
getFirebrowseCohortsQuery the Firebrowse web API for available cohorts
getFirebrowseDataTypesGet data types available from Firebrowse
getFirebrowseDateFormatReturns the date format used by the Firebrowse web API
getFirebrowseDatesQuery the Firebrowse web API for the available data...
getGenesGet or set globally accessible elements
getGenesFromSplicingEventsRetrieve genes based on given alternative splicing events
getGlobalGet or set globally accessible elements
getGroupsGet or set groups
getGtexTissuesGet GTEx tissues from given GTEx sample attributes
getHiddenGet or set hidden globally accessible elements
getHighlightedPointsGet or set points or regions for plots
getMatchingSamplesGet samples matching the given patients
getNumericsConvert a column to numeric if possible and ignore given...
getPatientFromSampleGet patients from given samples
getServerFunctionsMatches server functions from a given loader
getSplicingEventCoordinatesReturns the coordinates of interest for a given event type
getSplicingEventFromGenesRetrieve alternative splicing events based on given genes
getSplicingEventTypesSplicing event types available
getUiFunctionsMatches user interface (UI) functions from a given loader
getValidEventsFilters the events with valid elements according to the given...
getValuePerPatientAssign average sample values to their corresponding patients
ggplotServerLogic set to create an interactive ggplot
ggplotTooltipCreate the interface for the tooltip of a plot
ggplotUIInterface for interactive ggplot
globalSelectizeCreate a selectize input available from any page
groupByAttributeUser interface to group by attribute
groupByExpressionUser interface to group by subset expression
groupByGrepUser interface to group by grep expression
groupByIdUser interface to group by row
groupManipulationLogic server to manipulate data grouping
groupManipulationInputInterface to manipulate data grouping
groupPerElemAssign one group to each element
groupsServerOnceServer function for data grouping (one call)
hchart.survfitPlot survival curves using Highcharts
hc_scatterCreate scatter plot
inclusionLevelsInterfaceInterface to quantify alternative splicing
inlineDialogAlert in the style of a dialogue box with a button
insideFileGet psichomics file inside a given directory
isFileCheck if files exist
isFirebrowseUpCheck whether the Firebrowse web API is running
isRStudioServerCheck if running in RStudio Server
is.wholeCheck if a number is whole
joinEventsPerTypeFull outer join all given events based on select columns
junctionStringString used to search for matches in a junction...
kruskalPerform Kruskal's test and return interface to show the...
labelBasedOnCutoffLabel groups based on a given cutoff
levenePerform Levene's test and return interface to show the...
leveneTestLevene's test
linkToArticleInterface that directs users to original article
linkToRunJSLink to run arbitrary JavaScript code
listAllAnnotationsList alternative splicing annotation files available, as well...
listSplicingAnnotationsList the alternative splicing annotation files available
loadAnnotationLoad alternative splicing annotation from 'AnnotationHub'
loadByCheck if a given function should be loaded by the calling...
loadCustomSplicingAnnotationSetSet of functions to load a custom alternative splicing...
loadedDataModalCreate a modal warning the user of already loaded data
loadFileLoads a file according to its format
loadFileFormatsLoads file formats
loadFirebrowseDataDownloads and processes data from the Firebrowse web API and...
loadFirebrowseFoldersLoad Firebrowse folders
loadGeneExpressionSetSet of functions to load splicing quantification
loadGtexDataLoad GTEx data
loadGtexDataShinyShiny wrapper to load GTEx data
loadGtexFileLoad GTEx file
loadLocalFilesLoad local files
loadSplicingQuantificationSetSet of functions to load splicing quantification
loadSRAprojectDownload and load SRA projects
loadTCGAsampleMetadataPrepare TCGA sample metadata from loaded datasets
matchGroupPatientsAndSamplesMatch patients and samples in a group
matchSplicingEventsWithGenesMatch splicing events with respective genes
missingDataModalMissing information modal template
modTabPanelModified 'tabPanel' function to show icon and title
navSelectizeCreate a special selectize input in the navigation bar
noinfoInterface when no information could be retrieved
normaliseGeneExpressionFilter and normalise gene expression
operateOnGroupsSet operations on groups
optimalSurvivalCutoffCalculate optimal data cutoff that best separates survival...
optimSurvDiffSetOptimal survival difference given an inclusion level cutoff...
parseCategoricalGroupsParse categorical columns in a data frame
parseDateResponseParse the date from a response
parseFirebrowseMetadataQuery the Firebrowse web API for metadata
parseMatsEventParse alternative splicing events from MATS
parseMatsGenericParse junctions of an alternative splicing event from MATS...
parseMisoAnnotationGet events from alternative splicing annotation
parseMisoEventParse an alternative splicing event from MISO
parseMisoEventIDMatch MISO's splicing event IDs with the IDs present in the...
parseMisoGenericParse junctions of an event from MISO according to event type
parseMisoIdParse MISO's alternative splicing event identifier
parseSampleGroupsReturn the type of a given sample
parseSplicingEventParse an alternative splicing event based on a given...
parseSuppaEventParses splicing events of a specific event type from SUPPA
parseSuppaGenericParse junctions of an event from SUPPA
parseTcgaSampleInfoParse sample information from TCGA samples
parseUniprotXMLParse XML from UniProt's RESTful service
parseUrlsFromFirebrowseResponseRetrieve URLs from a response to a Firebrowse data query
parseValidFileParse file given a list of file formats
parseVastToolsEventParses an alternative splicing event from VAST-TOOLS
parseVastToolsSEParse junctions of an event from VAST-TOOLS according to...
patientMultiMatchWarningHelper text to explain what happens when a patient matches...
performICAPerform independent component analysis after processing...
performPCAPerform principal component analysis after processing missing...
plotClustersAdd clusters to 'highchart' object
plotCorrelationPlot correlations
plotDistributionPlot distribution through a density plot
plotGroupIndependencePlot -log10(p-values) of the results obtained after multiple...
plotICACreate multiple scatterplots from ICA
plotPCACreate a scatterplot from a PCA object
plotPointsStyleInterface to modify the style of the plot points
plotProteinPlot protein features
plotSingleICACreate a scatterplot for ICA
plotSurvivalCurvesPlot survival curves
plottableXrangesHTML code to plot a X-ranges series
plotTranscriptsPlot transcripts
plotVarianceCreate the explained variance plot
prepareAnnotationFromEventsPrepare annotation from alternative splicing events
prepareEventPlotOptionsPrepare event plot options
prepareFileBrowserPrepare file browser dialogue and update the input's value...
prepareFirebrowseArchivesPrepares Firebrowse archives in a given directory
prepareSRAmetadataPrepare files to be loaded into psichomics
prepareWordBreakCreate word break opportunities (for HTML) using given...
processButtonStyle button used to initiate a process
processDatasetNamesProcess dataset names
processSurvDataProcess survival data to calculate survival curves
processSurvivalCheck if survival analyses successfully completed or returned...
processSurvTermsProcess survival curves terms to calculate survival curves
psichomicsStart graphical interface of psichomics
pubmedUIReturn the interface of relevant PubMed articles for a given...
quantifySplicingQuantify alternative splicing events
quantifySplicingSetSet of functions to quantify alternative splicing
queryEnsemblQuery the Ensembl REST API
queryEnsemblByEventQuery information from Ensembl by a given alternative...
queryEnsemblByGeneQuery information from Ensembl by a given gene
queryFirebrowseDataQuery the Firebrowse web API for TCGA data
queryPubMedQuery the PubMed REST API
queryUniprotQuery the UniProt REST API
readAnnotRead custom or remote annotation
readFileLoad local file
reduceDimensionalityReduce dimensionality after processing missing values from...
renameDuplicatedRename vector to avoid duplicated values with another vector
renameGroupsRename duplicated names from a new group
renderDataTableSparklinesRender a data table with sparkline HTML elements
renderGeneticInfoRender genetic information
renderGroupInterfaceRender group interface
renderProteinInfoRender protein information
rm.nullFilter NULL elements from vector or list
roundDigitsRound by the given number of digits
roundMinDownRound down/up the minimum/maximum value
rowMeansCalculate mean for each row of a matrix
rowVarsCalculate variance for each row of a matrix
selectGroupsUIGroup selection
selectizeGeneInputCreate input to select a gene
setFirebrowseDataSet data from Firebrowse
setLocalDataLoad local files
setOperationPerform set operations on selected groups
setOperationIconCreate an icon based on set operations
showAlertShow or remove an alert
showGroupsTablePresent groups table
sidebarSidebar without a well
signifDigitsGet number of significant digits
singleDiffAnalysesPerform statistical analysis on a given splicing event
sortCoordinatesSort coordinates for some event types
spearmanPerform Spearman's test and return interface to show the...
startProcessSignal the program that a process is starting
startProgressCreate a progress object
styleModalStyle and show a modal
subsetGeneExpressionFromMatchingGenesSubset gene expression based on (full or partial) matching...
survdiff.survTermsTest differences between survival curves
survfit.survTermsCompute estimates of survival curves
tabDatasetCreates a 'tabPanel' template for a 'datatable' with a title...
table2htmlCreate HTML table from data frame or matrix
tableRowCreate a row for a HTML table
testGroupIndependenceMultiple independence tests between reference groups and list...
testSingleIndependenceMultiple independence tests between a reference group and...
testSurvivalTest the survival difference between groups of patients
testSurvivalCutoffTest the survival difference between two survival groups...
textSuggestionsCreate script for auto-completion of text input
toJSarrayConvert vector of values to JavaScript array
transformDataTransform data in data frame
transformOptionsShow variable transformation(s)
transformValuesTransform values as per a given type of transformation
trimWhitespaceTrims whitespace from a word
ttestPerform unpaired t-test analysis and return interface to show...
uniqueByCheck unique rows of a data frame based on a set of its...
updateClinicalParamsUpdate available clinical attributes when the clinical data...
updateFileBrowserInputChange the value of a fileBrowserInput on the client
updateProgressUpdate a progress object
vennEventsCompare the number of events from the different programs in a...
wilcoxPerform Wilcoxon analysis and return interface to show the...
psichomics documentation built on Dec. 4, 2018, 6:01 p.m.