Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation


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Documentation for package ‘psichomics’ version 1.6.2

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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