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General functions

psichomics()
Start graphical interface of psichomics
parseSplicingEvent()
Parse alternative splicing event identifier
getSplicingEventData()
Get splicing event information for given alternative splicing quantification data
getSplicingEventFromGenes() getGenesFromSplicingEvents()
Get alternative splicing events from genes or vice-versa
plotSplicingEvent()
Plot diagram of alternative splicing events
parseCategoricalGroups()
Parse categorical columns in a data frame
getDownloadsFolder()
Get the path to the Downloads folder

TCGA data retrieval

Retrieve TCGA data using Firebrowse API

isFirebrowseUp()
Check if FireBrowse API is running
getTCGAdataTypes() getTCGAdates() getTCGAcohorts()
Get available parameters for TCGA data
loadTCGAdata()
Download and process TCGA data
parseTCGAsampleTypes() parseTCGAsampleInfo()
Parse sample information from TCGA sample identifiers

GTEx data retrieval

getGtexDataTypes() getGtexReleases()
Get GTEx data information
getGtexTissues()
Get GTEx tissues from given GTEx sample attributes
loadGtexData()
Download and load GTEx data

SRA data retrieval

loadSRAproject()
Download and load SRA projects via recount2

User-provided data loading

loadLocalFiles()
Load local files
prepareSRAmetadata() prepareJunctionQuant() prepareGeneQuant()
Prepare user-provided files to be loaded into psichomics

Gene expression pre-processing

plotRowStats()
Plot row-wise statistics
plotGeneExprPerSample()
Plot distribution of gene expression per sample
plotLibrarySize()
Plot library size
filterGeneExpr()
Filter genes based on their expression
normaliseGeneExpression() normalizeGeneExpression()
Filter and normalise gene expression
convertGeneIdentifiers()
Convert gene identifiers

PSI quantification and filtering

getSplicingEventTypes()
Get supported splicing event types
listSplicingAnnotations()
List alternative splicing annotations
loadAnnotation()
Load alternative splicing annotation from AnnotationHub
quantifySplicing()
Quantify alternative splicing events
discardLowCoveragePSIvalues()
Remove alternative splicing quantification values based on coverage
filterPSI()
Filter alternative splicing quantification
plotRowStats()
Plot row-wise statistics

Custom alternative splicing annotation

parseSuppaAnnotation() parseVastToolsAnnotation() parseMisoAnnotation() parseMatsAnnotation()
Parse events from alternative splicing annotation
prepareAnnotationFromEvents()
Prepare annotation from alternative splicing events

Data Grouping

createGroupByAttribute()
Split elements into groups based on a given column of a dataset
filterGroups()
Filter groups with less data points than the threshold
groupPerElem()
Assign one group to each element
getGeneList()
Get curated, literature-based gene lists
getSampleFromSubject()
Get samples matching the given subjects
getSubjectFromSample()
Get subjects from given samples
testGroupIndependence()
Multiple independence tests between reference groups and list of groups
plotGroupIndependence()
Plot -log10(p-values) of the results obtained after multiple group independence testing

Principal component analysis (PCA)

performPCA()
Perform principal component analysis after processing missing values
plotPCAvariance()
Create the explained variance plot from a PCA
calculateLoadingsContribution()
Calculate the contribution of PCA loadings to the selected principal components
plotPCA()
Create a scatterplot from a PCA object

Independent component analysis (ICA)

performICA()
Perform independent component analysis after processing missing values
plotICA()
Create multiple scatterplots from ICA

Differential analyses

diffAnalyses()
Perform statistical analyses
plotDistribution()
Plot sample distribution

Gene expression and alternative splicing correlation

correlateGEandAS()
Correlate gene expression data against alternative splicing quantification
`[`(<GEandAScorrelation>) plot(<GEandAScorrelation>) print(<GEandAScorrelation>) as.table(<GEandAScorrelation>)
Display results of correlation analyses

Survival analysis

getAttributesTime()
Get time values for given columns in a clinical dataset
processSurvTerms()
Process survival curves terms to calculate survival curves
survfit(<survTerms>)
Create survival curves
survdiffTerms()
Test Survival Curve Differences
plotSurvivalCurves()
Plot survival curves
testSurvival()
Test the survival difference between groups of subjects
assignValuePerSubject()
Assign average sample values to their corresponding subjects
labelBasedOnCutoff()
Label groups based on a given cutoff
optimalSurvivalCutoff()
Calculate optimal data cutoff that best separates survival curves
plotSurvivalPvaluesByCutoff()
Plot p-values of survival difference between groups based on multiple cutoffs

Gene, transcript and protein annotation retrieval

queryEnsemblByGene() queryEnsemblByEvent()
Query information from Ensembl
ensemblToUniprot()
Convert from Ensembl to UniProt identifier
plotProtein()
Plot protein features
plotTranscripts()
Plot transcripts