# Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

## Documentation for package ‘psichomics’ version 1.0.8

- 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 --

addTCGAdata | Creates a UI set with options to add data from TCGA/Firehose
analysesServer | Server logic for the analyses
analysesUI | User interface for the data analyses
appServer | Server function
appUI | The user interface (ui) controls the layout and appearance of the app All the CSS modifications are in the file "shiny/www/styles.css"
articleUI | Return the interface to display an article

## -- B --

basicStats | Basic statistics performed on data
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
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
createDataTab | Render a specific data tab (including data table and related interface)
createDensitySparklines | Create density sparklines for inclusion levels
createGroup | Prepare to create group according to specific details
createGroupByAttribute | Create groups with the indexes from the unique values of a given column from a dataset
createGroupByColumn | Create groups with the indexes from the unique values of a given column from a dataset
createGroupById | Create groups from a given string of rows
createGroupFromInput | Set new groups according to the user input
createJunctionsTemplate | Creates a template of alternative splicing junctions

## -- D --

dataServer | Server logic of the data module
dataUI | User interface of the data module
diffAnalyses | Perform selected statistical analyses on multiple splicing events
diffSplicingEventServer | Server logic for the analyses of a single alternative splicing event
diffSplicingEventUI | Interface for the analysis of an alternative splicing event
diffSplicingServer | Server logic for the differential splicing analyses
diffSplicingTableServer | Server logic of the exploratory differential analyses
diffSplicingTableUI | Interface for differential analyses on all splicing events
diffSplicingUI | User interface for the differential splicing analyses
disableTab | Disable a tab from the navbar
downloadFiles | Download files to a given directory

## -- E --

echoProgress | Echo progress to console using 'cat'
enableTab | Enable a tab from the navbar
endProcess | Signal the program that a process has ended
ensemblToUniprot | Convert a protein's Ensembl identifier to UniProt identifier
errorAlert | Show an alert
errorModal | Style and show a modal
escape | Escape symbols for use in regular expressions
export_highcharts | Add an exporting feature to a 'highcharts' object

## -- F --

filterGroups | Filter groups with less data points than the threshold
firebrowseUI | User interface of the TCGA/Firebrowse loader
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 --

getActiveDataset | Get selected dataset
getAssemblyVersion | Get the assembly version of a data category
getAutoNavigation | Get if history browsing is automatic
getCategories | Get available data categories
getCategory | Get selected data category
getCategoryData | Get data of selected data category
getClinicalData | Get clinical data of the data category
getClinicalMatchFrom | Get clinical matches from a given data type
getColumnsTime | Retrieve the time for given columns in a clinical dataset
getCores | Get number of cores to use
getData | Get global data
getDataRows | Get rows of a data frame between two row indexes
getDifferentialAnalyses | Get the table of differential analyses of a data category
getDifferentialAnalysesSurvival | Get the table of differential analyses' survival data of a data category
getDownloadsFolder | Get the Downloads folder of the user
getEvent | Get selected alternative splicing event's identifer
getFirehoseCohorts | Query the Firehose API for the cohorts available
getFirehoseDataTypes | Get data types available from Firehose
getFirehoseDateFormat | Returns the date format used by the Firehose API
getFirehoseDates | Query the Firehose API for the datestamps of the data available and parse the response
getGlobal | Get data from global data
getGroupsFrom | Get groups from a given data type
getInclusionLevels | Get alternative splicing quantification of the selected data category
getInclusionLevelsPCA | Get principal component analysis based on inclusion levels
getJunctionQuantification | Get junction quantification data
getMatchingSamples | Search samples in the clinical dataset and return the ones matching the given index
getNumerics | Convert a column to numeric if possible and ignore given columns composed of lists
getPatientFromSample | Match given sample identifiers and return the respective row in clinical data
getPatientId | Get the identifier of patients for a given category
getPrecision | Get number of decimal places
getPSIperPatient | Assign alternative splicing quantification to patients based on their samples
getSampleId | Get the identifier of samples for a given category
getSampleInfo | Get sample information of the selected data category
getSelectedGroups | Get selected groups for a given group selection element
getServerFunctions | Matches server functions from a given loader
getSignificant | Get number of significant digits
getSpecies | Get the species of a data category
getSplicingEventCoordinates | Returns the coordinates of interest for a given event type
getSplicingEventTypes | Splicing event types available
getUiFunctions | Matches user interface (UI) functions from a given loader
getURLtoDownload | Get the URL links to download
getValidEvents | Filters the events with valid elements according to the given validator
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
groupPerPatient | Assign one group to each patient
groupPerSample | Assign one group to each sample
groupsServer | Server function for data grouping
groupsServerOnce | Server function for data grouping (one call)
groupsUI | Creates UI elements for the grouping feature
gtexDataServer | Server logic to load GTEx data
gtexDataUI | Interface to load GTEx data

## -- H --

hchart.survfit | Plot survival curves using Highcharts
hc_scatter | Create scatter plot

## -- I --

inclusionLevelsInterface | Interface to quantify alternative splicing
inclusionLevelsServer | Server logic of the alternative splicing event quantification module
inclusionLevelsUI | Interface of the alternative splicing event quantification module
infoModal | Style and show a modal
infoServer | Server logic
infoUI | Information's user interface
insideFile | Get psichomics file inside a given directory
is.whole | Check if a number is whole
isFirehoseUp | Check if the Firehose API is running

## -- 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 cut-off
levene | Perform Levene's test and return interface to show the results
leveneTest | Levene's test
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
loadedDataModal | Create a modal warning the user of already loaded data
loadFile | Loads a file according to its format
loadFileFormats | Loads file formats
loadFirehoseData | Downloads and processes data from the Firehose API and loads it into R
loadFirehoseFolders | Load Firehose folders
loadGtexData | Load GTEx data given input
loadLocalFiles | Load local files
loadRequiredData | Missing information modal template
localDataServer | Server logic to load local data
localDataUI | Interface to load local data

## -- M --

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 navigatin bar
noinfo | Interface when no information could be retrieved

## -- O --

operateOnGroups | Set operations on groups
optimalPSIcutoff | Calculate optimal alternative splicing quantification cut-off to separate survival curves
optimSurvDiff | Optimal survival difference given an inclusion level cut-off for a specific alternative splicing event
optimSurvDiffOptions | Interface for calculating optimal cut-off and p-value for survival curves differences

## -- P --

parseDateResponse | Parse the date from a response
parseFirehoseMetadata | Query the Firehose API for metadata and parse the response
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
parseTcgaSampleInfo | Parse and prepare sample information from TCGA samples
parseUniprotXML | Parse XML from Uniprot's RESTful service
parseUrlsFromFirehoseResponse | Retrieve URLs from a response to a Firehose 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
pcaServer | Server logic for the principal component analysis
pcaUI | User interface of the principal component analysis
performPCA | Perform principal component analysis after processing missing values from data frame
plotDistribution | Plot distribution through a density plot
plotMiniSurvivalCurves | Perform and plot survival curves
plotPCA | Create a scatterplot from a PCA object
plotProtein | Plot protein features
plotSurvivalCurves | Plot survival curves
plotTranscripts | Plot transcripts
plotVariance | Create the explained variance plot
prepareAnnotationFromEvents | Prepare annotation from alternative splicing events
prepareFirehoseArchives | Prepares Firehose archives in a given directory
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
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
queryFirehoseData | Query the Firehose API for TCGA data
queryPubMed | Query the PubMed REST API
queryUniprot | Query the Uniprot REST API

## -- R --

readFile | Load local file
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
rm.null | Filter NULL elements from vector or list
roundDigits | Round by the given number of digits
rowVar | Sample variance by row

## -- S --

selectGroupsServer | Group selection logic
selectGroupsUI | Group selection interface
setActiveDataset | Set active dataset
setAssemblyVersion | Set the assembly version of a data category
setAutoNavigation | Set if history browsing is automatic
setCategory | Set data category
setClinicalMatchFrom | Set clinical matches from a given data type
setCores | Set number of cores
setData | Set data of the global data
setDifferentialAnalyses | Set the table of differential analyses of a data category
setDifferentialAnalysesSurvival | Set the table of differential analyses' survival data of a data category
setEvent | Set event
setFirehoseData | Set data from Firehose
setGlobal | Set element as globally accessible
setGroupsFrom | Set groups from a given data type
setInclusionLevels | Set inclusion levels for a given data category
setInclusionLevelsPCA | Get principal component analysis based on inclusion levels
setLocalData | Load local files
setPatientId | Set the identifier of patients for a data category
setPrecision | Set number of decimal places
setSampleId | Set the identifier of samples for a data category
setSampleInfo | Set sample information for a given data category
setSignificant | Set number of significant digits
setSpecies | Set the species of a data category
settingsServer | Server logic of the settings
settingsUI | User interface of the settings
setURLtoDownload | Set URL links to download
showAlert | Show an alert
showGroupsTable | Present groups table
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
survdiff.survTerms | Test difference between two or more survival curves using processed survival terms
survfit.survTerms | Compute estime of a survival curve using processed survival terms
survivalServer | Server logic of survival analysis
survivalUI | User interface of survival analysis

## -- T --

tabDataset | Creates a tabPanel template for a datatable with a title and description
templateServer | Server logic of template
templateUI | User interface of template
testSurvival | Test the survival difference between survival groups
testSurvivalCutoff | Test the survival difference between two survival groups given a cutoff
textSuggestions | Create script for autocompletion of text input
timePerPatient | Get all columns matching a given string and return a single vector with the max time for each patient if available
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
updateProgress | Update a progress object

## -- V --

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

## -- W --

warningAlert | Show an alert
warningModal | Style and show a modal
wilcox | Perform Wilcoxon analysis and return interface to show the results