Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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Documentation for package ‘psichomics’ version 1.16.0

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.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 distribution using a density plot
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