# Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

## Documentation for package ‘psichomics’ version 1.12.0

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

## Help Pages

as.table.GEandAScorrelation | Display results of correlation analyses
assignValuePerPatient | Assign average sample values to their corresponding patients
assignValuePerSubject | Assign average sample values to their corresponding patients
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
createGroupByColumn | Split elements into groups based on a given column of a dataset
diffAnalyses | Perform statistical analyses
ensemblToUniprot | Convert an Ensembl identifier to the respective 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 | Retrieve the time for given columns in a clinical dataset
getColumnsTime | Retrieve the time for given columns in a clinical dataset
getDownloadsFolder | Get the Downloads folder of the user
getFirebrowseCohorts | Query the Firebrowse web API
getFirebrowseDataTypes | Get data types available from Firebrowse
getFirebrowseDates | Query the Firebrowse web API
getFirehoseDataTypes | Get data types available from Firebrowse
getGeneList | Get pre-created, literature-based gene list
getGenesFromSplicingEvents | Get alternative splicing events from genes or vice-versa
getGtexTissues | Get GTEx tissues from given GTEx sample attributes
getMatchingSamples | Get samples matching the given patients
getPatientFromSample | Get patients from given samples
getPSIperPatient | Assign average sample values to their corresponding patients
getSampleFromPatient | Get samples matching the given patients
getSampleFromSubject | Get samples matching the given patients
getSplicingEventFromGenes | Get alternative splicing events from genes or vice-versa
getSplicingEventTypes | Splicing event types available
getSubjectFromSample | Get patients from given samples
getValuePerPatient | Assign average sample values to their corresponding patients
getValuePerSubject | Assign average sample values to their corresponding patients
groupByAttribute | Data grouping interface
groupByExpression | Data grouping interface
groupByGrep | Data grouping interface
groupById | Data grouping interface
groupByPreMadeList | Data grouping interface
groupPerElem | Assign one group to each element
groupPerPatient | Assign one group to each element
groupPerSample | Assign one group to each element
isFirebrowseUp | Check whether the Firebrowse web API is running
labelBasedOnCutoff | Label groups based on a given cutoff
listSplicingAnnotations | List the alternative splicing annotation files available
loadAnnotation | Load alternative splicing annotation from 'AnnotationHub'
loadFirebrowseData | Downloads and processes data from the Firebrowse web API and loads it into R
loadGtexData | Load GTEx data
loadLocalFiles | Load local files
loadSRAproject | Download and load SRA projects
normaliseGeneExpression | Filter and normalise gene expression
optimalPSIcutoff | Calculate optimal data cutoff that best separates survival curves
optimalSurvivalCutoff | Calculate optimal data cutoff that best separates survival curves
parseCategoricalGroups | Parse categorical columns in a data frame
parseMatsAnnotation | Get events from alternative splicing annotation
parseMisoAnnotation | Get events from alternative splicing annotation
parseSampleGroups | Return the type of a given sample
parseSplicingEvent | Parse an alternative splicing event based on a given identifier
parseSuppaAnnotation | Get events from alternative splicing annotation
parseTCGAsampleInfo | Parse sample information from TCGA samples
parseTcgaSampleInfo | Parse sample information from TCGA samples
parseVastToolsAnnotation | Get 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 through 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
plotPCA | Create a scatterplot from a PCA object
plotProtein | Plot protein features
plotRowStats | Plot sample statistics per row
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 files to be loaded into psichomics
prepareGeneQuantSTAR | Prepare files to be loaded into psichomics
prepareJunctionQuant | Prepare files to be loaded into psichomics
prepareJunctionQuantSTAR | Prepare files to be loaded into psichomics
prepareSRAmetadata | Prepare 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 local file
rowMeans | Calculate mean or variance for each row of a matrix
rowVars | Calculate mean or variance for each row of a matrix
survdiffTerms | Test Survival Curve Differences
survfit.survTerms | Create survival curves
testGroupIndependence | Multiple independence tests between reference groups and list of groups
testSurvival | Test the survival difference between groups of patients
[.GEandAScorrelation | Subset correlation results between gene expression and splicing quantification