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

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 distribution using a density plot

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