Package index • psichomics

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