# Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

## Documentation for package ‘psichomics’ version 1.20.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.onAttach | Print startup message
as.table.GEandAScorrelation | Display results of correlation analyses
assignValuePerPatient | Assign average sample values to their corresponding subjects
assignValuePerSubject | Assign average sample values to their corresponding subjects
calculateLoadingsContribution | Calculate the contribution of PCA loadings to the selected principal components
colSums-method | Sum columns using an 'EList-class' object
convertGeneIdentifiers | Convert gene identifiers
correlateGEandAS | Correlate gene expression data against alternative splicing quantification
createGroupByAttribute | Split elements into groups based on a given column of a dataset
diffAnalyses | Perform statistical analyses
discardLowCoveragePSIvalues | Remove alternative splicing quantification values based on coverage
ensemblToUniprot | Convert from Ensembl to UniProt identifier
filterGeneExpr | Filter genes based on their expression
filterGroups | Filter groups with less data points than the threshold
filterPSI | Filter alternative splicing quantification
getAttributesTime | Get time values for given columns in a clinical dataset
getDownloadsFolder | Get the path to the Downloads folder
getFirebrowseCohorts | Get available parameters for TCGA data
getFirebrowseDataTypes | Get available parameters for TCGA data
getFirebrowseDates | Get available parameters for TCGA data
getGeneList | Get curated, literature-based gene lists
getGenesFromSplicingEvents | Get alternative splicing events from genes or vice-versa
getGtexDataTypes | Get GTEx data information
getGtexReleases | Get GTEx data information
getGtexTissues | Get GTEx tissues from given GTEx sample attributes
getMatchingSamples | Get samples matching the given subjects
getPatientFromSample | Get subjects from given samples
getSampleFromPatient | Get samples matching the given subjects
getSampleFromSubject | Get samples matching the given subjects
getSplicingEventData | Get splicing event information for given alternative splicing quantification data
getSplicingEventFromGenes | Get alternative splicing events from genes or vice-versa
getSplicingEventTypes | Get supported splicing event types
getSubjectFromSample | Get subjects from given samples
getTCGAcohorts | Get available parameters for TCGA data
getTCGAdataTypes | Get available parameters for TCGA data
getTCGAdates | Get available parameters for TCGA data
getValuePerPatient | Assign average sample values to their corresponding subjects
getValuePerSubject | Assign average sample values to their corresponding subjects
groupPerElem | Assign one group to each element
isFirebrowseUp | Check if FireBrowse API is running
labelBasedOnCutoff | Label groups based on a given cutoff
listSplicingAnnotations | List alternative splicing annotations
loadAnnotation | Load alternative splicing annotation from 'AnnotationHub'
loadFirebrowseData | Download and process TCGA data
loadGtexData | Download and load GTEx data
loadLocalFiles | Load local files
loadSRAproject | Download and load SRA projects via recount2
loadTCGAdata | Download and process TCGA data
normaliseGeneExpression | Filter and normalise gene expression
normalizeGeneExpression | Filter and normalise gene expression
optimalSurvivalCutoff | Calculate optimal data cutoff that best separates survival curves
parseCategoricalGroups | Parse categorical columns in a data frame
parseMatsAnnotation | Parse events from alternative splicing annotation
parseMisoAnnotation | Parse events from alternative splicing annotation
parseSampleGroups | Parse sample information from TCGA sample identifiers
parseSplicingEvent | Parse alternative splicing event identifier
parseSuppaAnnotation | Parse events from alternative splicing annotation
parseTCGAsampleInfo | Parse sample information from TCGA sample identifiers
parseTcgaSampleInfo | Parse sample information from TCGA sample identifiers
parseTCGAsampleTypes | Parse sample information from TCGA sample identifiers
parseVastToolsAnnotation | Parse events from alternative splicing annotation
performICA | Perform independent component analysis after processing missing values
performPCA | Perform principal component analysis after processing missing values
plot.GEandAScorrelation | Display results of correlation analyses
plotCorrelation | Display results of correlation analyses
plotDistribution | Plot sample distribution
plotGeneExprPerSample | Plot distribution of gene expression per sample
plotGroupIndependence | Plot '-log10(p-values)' of the results obtained after multiple group independence testing
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
plotProtein | Plot protein features
plotRowStats | Plot row-wise statistics
plotSplicingEvent | Plot diagram of alternative splicing events
plotSurvivalCurves | Plot survival curves
plotSurvivalPvaluesByCutoff | Plot p-values of survival difference between groups based on multiple cutoffs
plotTranscripts | Plot transcripts
plotVariance | Create the explained variance plot from a PCA
prepareAnnotationFromEvents | Prepare annotation from alternative splicing events
prepareGeneQuant | Prepare user-provided files to be loaded into psichomics
prepareJunctionQuant | Prepare user-provided files to be loaded into psichomics
prepareSRAmetadata | Prepare user-provided files to be loaded into psichomics
print.GEandAScorrelation | Display results of correlation analyses
processSurvTerms | Process survival curves terms to calculate survival curves
psichomics | Start graphical interface of psichomics
quantifySplicing | Quantify alternative splicing events
queryEnsemblByEvent | Query information from Ensembl
queryEnsemblByGene | Query information from Ensembl
readFile | Load psichomics-specific file
survdiffTerms | Test Survival Curve Differences
survfit.survTerms | Create survival curves
t.sticky | Preserve attributes of 'sticky' objects when extracting or transposing object
testGroupIndependence | Multiple independence tests between reference groups and list of groups
testSurvival | Test the survival difference between groups of subjects
[.GEandAScorrelation | Display results of correlation analyses
[.sticky | Preserve attributes of 'sticky' objects when extracting or transposing object