Man pages for psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
| addObjectAttrs | Set attributes to an object |
| addTCGAdata | Creates a UI set with options to add data from... |
| analysesTableSet | Set of functions to render differential analyses (plot and... |
| 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 |
| assignValuePerSubject | Assign average sample values to their corresponding subjects |
| basicStats | Basic statistics performed on data |
| blendColours | Blend two HEX colours |
| browserHistory | Enable history navigation |
| calculateInclusionLevels | Calculate inclusion levels using alternative splicing event... |
| calculateLoadingsContribution | Calculate the contribution of PCA loadings to the selected... |
| checkFileFormat | Checks the format of a file |
| checkFirebrowse | Return an user interface depending on the status of the... |
| checkGroupType | Check type of groups within file |
| checkIntegrity | Compute the 32-byte 'MD5' hashes of one or more files and... |
| checkSurvivalInput | Prepare survival terms in case of valid input |
| clusterICAset | Server logic for clustering ICA data |
| clusterSet | Server logic for clustering PCA data |
| colourInputMod | Modified colour input with 100% width |
| colSums-EList-method | Sum columns using an 'EList-class' object |
| convertGeneIdentifiers | Convert gene identifiers |
| correlateGEandAS | Correlate gene expression data against alternative splicing... |
| createDataTab | Render a specific data tab (including data table and related... |
| 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... |
| 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 |
| customRowMeans | Calculate statistics for each row or column of a matrix |
| diagramSplicingEvent | Prepare SVG diagram of alternative splicing events |
| diffAnalyses | Perform statistical analyses |
| diffExpressionSet | Set of functions to perform differential analyses |
| diffSplicingSet | Set of functions to perform differential analyses |
| disableTab | Enable or disable a tab from the 'navbar' |
| discardLowCoveragePSIvalues | Remove alternative splicing quantification values based on... |
| discardOutsideSamplesFromGroups | Discard grouped samples if not within a sample vector |
| display | Display characters in the command-line |
| dot-onAttach | Print startup message |
| downloadFiles | Download files to a given directory |
| ensemblToUniprot | Convert from Ensembl to UniProt identifier |
| escape | Escape symbols for use in regular expressions |
| eventPlotOptions | Options for event plotting |
| exportGroupsToFile | Export groups to a file |
| export_highcharts | Add an exporting feature to a 'highcharts' object |
| fileBrowser | Interactive folder selection using a native dialogue |
| fileBrowserInput | File browser input |
| filterGeneExpr | Filter genes based on their expression |
| filterGroups | Filter groups with less data points than the threshold |
| filterPSI | Filter alternative splicing quantification |
| findASeventsFromGene | Find splicing events based on given genes |
| findEventData | Look for event data in input |
| geneExprFileInput | File input for gene expression |
| geneExprSurvSet | Logic set to perform survival analysis based on gene... |
| geNormalisationFilteringInterface | Interface to normalise and filter gene expression |
| getAttributesTime | Get time values for given columns in a clinical dataset |
| getClinicalDataForSurvival | Retrieve clinical data based on attributes required for... |
| getClinicalMatchFrom | Get or set clinical matches from a given data type |
| 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... |
| getDifferentialSplicing | Get or set differential splicing' elements for a data... |
| getDownloadsFolder | Get the path to the Downloads folder |
| getFirebrowseDateFormat | Returns the date format used by the Firebrowse API |
| getGeneList | Get curated, literature-based gene lists |
| getGlobal | Get or set globally accessible elements |
| getGroups | Get or set groups |
| getGtexDataTypes | Get GTEx data information |
| getGtexDataURL | Get links to download GTEx data |
| 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 |
| getNumerics | Convert a column to numeric if possible and ignore given... |
| getSampleFromSubject | Get samples matching the given subjects |
| getServerFunctions | Matches server functions from a given loader |
| getSplicingEventCoordinates | Returns the coordinates of interest for a given event type |
| getSplicingEventData | Get splicing event information for given alternative splicing... |
| getSplicingEventFromGenes | Get alternative splicing events from genes or vice-versa |
| getSplicingEventTypes | Get supported splicing event types |
| getSubjectFromSample | Get subjects from given samples |
| getTCGAdataTypes | Get available parameters for TCGA data |
| getUiFunctions | Matches user interface (UI) functions from a given loader |
| getValidEvents | Filters the events with valid elements according to the given... |
| 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 | Data grouping interface |
| groupManipulation | Logic server to manipulate data grouping |
| groupManipulationInput | Interface to manipulate data grouping |
| groupPerElem | Assign one group to each element |
| groupsServerOnce | Server function for data grouping (one call) |
| hchart.survfit | Plot survival curves |
| hc_scatter | Create scatter plot |
| HTMLfast | Faster version of 'shiny::HTML' |
| importGroupsFrom | Import groups from a file |
| inclusionLevelsFilterInterface | Interface to filter alternative splicing |
| inclusionLevelsInterface | Interface to quantify alternative splicing |
| inlineDialog | Alert in the style of a dialogue box with a button |
| insideFile | Get psichomics file inside a given directory |
| isFile | Check if files exist |
| isFirebrowseUp | Check if Firebrowse API is running |
| isRStudioServer | Check if running in RStudio Server |
| is.whole | Check if a number is whole |
| joinEventsPerType | Full outer join all given events based on select columns |
| junctionString | String used to search for matches in a junction... |
| labelBasedOnCutoff | Label groups based on a given cutoff |
| leveneTest | Levene's test |
| linkToArticles | psichomics article's link interface |
| linkToRunJS | Link to run arbitrary JavaScript code |
| listAllAnnotations | List alternative splicing annotation files available, as well... |
| listSplicingAnnotations | List alternative splicing annotations |
| loadAnnotation | Load alternative splicing annotation from 'AnnotationHub' |
| loadBy | Check if a given function should be loaded by the calling... |
| loadCustomSplicingAnnotationSet | Set of functions to load a custom alternative splicing... |
| loadedDataModal | Warn user about loaded data |
| loadFile | Load file based on its format |
| loadFileFormats | Load supported file formats |
| loadFirebrowseFolders | Load Firebrowse folders |
| loadGeneExpressionSet | Set of functions to load splicing quantification |
| loadGtexData | Download and load GTEx data |
| loadGtexDataShiny | Shiny wrapper to load GTEx data |
| loadGtexFile | Load GTEx file |
| loadLocalFiles | Load local files |
| loadSplicingQuantificationSet | Set of functions to load splicing quantification |
| loadSRAproject | Download and load SRA projects via recount2 |
| loadTCGAdata | Download and process TCGA data |
| loadTCGAsampleMetadata | Prepare TCGA sample metadata from loaded datasets |
| matchGroupASeventsAndGenes | Match AS events and genes in a group |
| matchGroupSubjectsAndSamples | Match subjects and samples in a group |
| matchSplicingEventsWithGenes | Match splicing events with respective genes |
| missingDataModal | Missing information modal template |
| modTabPanel | Modified 'tabPanel' function to show icon and title |
| navSelectize | Create a special 'selectize' input in the navigation bar |
| normaliseGeneExpression | Filter and normalise gene expression |
| operateOnGroups | Set operations on groups |
| optimalSurvivalCutoff | Calculate optimal data cutoff that best separates survival... |
| optimSurvDiffSet | Optimal survival difference given an inclusion level cutoff... |
| parseCategoricalGroups | Parse categorical columns in a data frame |
| parseDateResponse | Parse the date from a response |
| parseFile | Parse file according to its format |
| parseFirebrowseMetadata | Query the Firebrowse API for metadata |
| parseMatsEvent | Parse alternative splicing events from MATS |
| parseMatsGeneric | Parse junctions of an alternative splicing event from MATS... |
| parseMisoAnnotation | Parse 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... |
| parseMisoGeneric | Parse junctions of an event from MISO according to event type |
| parseMisoId | Parse MISO's alternative splicing event identifier |
| parseSplicingEvent | Parse alternative splicing event identifier |
| parseSuppaEvent | Parses splicing events of a specific event type from SUPPA |
| parseSuppaGeneric | Parse junctions of an event from SUPPA |
| parseTcgaSampleInfo | Parse sample information from TCGA sample identifiers |
| parseUniprotXML | Parse XML from UniProt REST service |
| parseUrlsFromFirebrowseResponse | Retrieve URLs from a response to a Firebrowse data query |
| parseVastToolsEvent | Parses an alternative splicing event from VAST-TOOLS |
| parseVastToolsSE | Parse junctions of an event from VAST-TOOLS according to... |
| performICA | Perform independent component analysis after processing... |
| performPCA | Perform principal component analysis after processing missing... |
| plotClusters | Add clusters to 'highchart' object |
| plotDistribution | Plot distribution using a density plot |
| plot.GEandAScorrelation | Display results of correlation analyses |
| plotGeneExprPerSample | Plot distribution of gene expression per sample |
| plotGroupIndependence | Plot '-log10(p-values)' of the results obtained after... |
| plotICA | Create multiple scatterplots from ICA |
| plotLibrarySize | Plot library size |
| plotPCA | Create a scatterplot from a PCA object |
| plotPCAvariance | Create the explained variance plot from a PCA |
| plotPointsStyle | Interface to modify the style of the plot points |
| plotProtein | Plot protein features |
| plotRowStats | Plot row-wise statistics |
| plotSingleICA | Create a scatterplot for ICA |
| plotSplicingEvent | Plot diagram of alternative splicing events |
| plotSurvivalCurves | Plot survival curves |
| plotSurvivalPvaluesByCutoff | Plot p-values of survival difference between groups based on... |
| plottableXranges | HTML code to plot a X-ranges series |
| plotTranscripts | Plot transcripts |
| prepareAnnotationFromEvents | Prepare annotation from alternative splicing events |
| prepareEventPlotOptions | Prepare event plot options |
| prepareFileBrowser | Prepare file browser dialogue and update the input's value... |
| prepareFirebrowseArchives | Prepares Firebrowse archives in a given directory |
| prepareGenePresentation | Prepare presentation of multiple genes for the same splicing... |
| prepareJunctionQuantSTAR | Prepare user-provided files to be loaded into psichomics |
| preparePreMadeGroupForSelection | Prepare list of pre-made groups for a 'selectize' element |
| prepareSRAmetadata | Prepare user-provided files to be loaded into psichomics |
| prepareWordBreak | Create word break opportunities (for HTML) using given... |
| preserveAttributes | Preserve attributes when extracting values |
| processButton | Style button used to initiate a process |
| processDatasetNames | Process dataset names |
| processSRAdata | Process SRA quantification data |
| processSurvData | Process survival data to calculate survival curves |
| processSurvival | Check if survival analyses successfully completed or returned... |
| 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... |
| quantifySplicing | Quantify alternative splicing events |
| quantifySplicingSet | Set of functions to quantify alternative splicing |
| queryEnsembl | Query the Ensembl REST API |
| queryEnsemblByGene | Query information from Ensembl |
| queryFirebrowseData | Query the Firebrowse API for TCGA data |
| queryPubMed | Query the PubMed REST API |
| queryUniprot | Query the UniProt REST API |
| readAnnot | Read custom or remote annotation |
| readFile | Load psichomics-specific file |
| reduceDimensionality | Reduce dimensionality after processing missing values from... |
| renameDuplicated | Rename vector to avoid duplicated values with another vector |
| renameGroups | Rename duplicated names from a new group |
| renderBoxplot | Render boxplot |
| 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 a vector or a list |
| roundDigits | Round by the given number of digits |
| roundMinDown | Round down/up the minimum/maximum value |
| saveProcessedSRAdata | Save processed SRA data in file |
| selectGroupsUI | Group selection |
| selectizeGeneInput | Create input to select a gene |
| selectPreMadeGroup | Select pre-made groups from a selected item |
| setFirebrowseData | Set data from Firebrowse |
| setLocalData | Load local files |
| setOperation | Perform set operations on selected groups |
| setOperationIcon | Create an icon based on set operations |
| 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 |
| startProcess | Set the status of a process to style a given button |
| startProgress | Create, set and terminate a progress object |
| styleModal | Create a modal window |
| subjectMultiMatchWarning | Helper text to explain what happens when a subject matches... |
| subsetGeneExpressionFromMatchingGenes | Subset gene expression based on (full or partial) matching... |
| survdiffTerms | Test Survival Curve Differences |
| survfit.survTerms | Create survival curves |
| tabDataset | Creates a 'tabPanel' template for a 'datatable' with a title... |
| table2html | Create HTML table from data frame or matrix |
| tableRow | Create a row for a HTML table |
| testGroupIndependence | Multiple independence tests between reference groups and list... |
| testSingleIndependence | Multiple independence tests between a reference group and... |
| testSurvival | Test the survival difference between groups of subjects |
| testSurvivalCutoff | Test the survival difference between two survival groups... |
| 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 |
| t.sticky | Preserve attributes of 'sticky' objects when extracting or... |
| uniqueBy | Check unique rows of a data frame based on a set of its... |
| updateClinicalParams | Update available clinical attributes when the clinical data... |
| updateFileBrowserInput | Change the value of a 'fileBrowserInput()' on the client |
| vennEvents | Compare the number of events from the different programs in a... |
| wilcox | Perform and display statistical analysis |
