addHoverText            Add column with hover text to top table
arrangeTopTables        Arrange top tables
calcCorrelation         Calculate correlation
callBarplot             Create ggplot object with barplot
callHeatmap             Create ggplot object with heatmap
callLogRatioPlot        Create ggplot object with log ratio plot
callMAplot              Create ggplot object with MA plot
callScatterPlot         Create ggplot object with scatter plot
callVolcanoPlot         Create ggplot object with volcano plot
callWaterfallPlot       Create ggplot object with waterfall plot
cbindFill               Combine data.frames by columns allowing for
                        different number of rows.
checkCoef               Check coefficients
checkColumns            Check input fields
checkInput              Check input
colorBlindPalette       Color-blind palette
concatenateVars         Concatenate feature variables
createDataBarplot       Create table for barplot
createDataHeatmap       Create table for heatmap
createDataLogRatioPlot
                        Create table for log ratio plot
createDataMAplot        Create table for MA plot
createDataScatterPlot   Create table for the scatter plot
createDataUpsetPlot     Create data for upset plot
createDataVolcanoPlot   Create table for the volcano plot
createDataWaterfallPlot
                        Create data for waterfall plot
createExampleData       Create example limma-, edgeR-object or a list
                        of top tables.
createExpressionSet     Create ExpressionSet object from example data
createPairData          Create pairwise data
createSampleAnnotation
                        Create sample annotation from example data
createTopTableGenesOfInterest
                        Create table for genes of interest
daHeatmapLogFC          Heatmap of log fold-changes
daLogRatioPlot          Plot log ratios
daMAplot                MA plot
daScatterPlot           Scatter plot
daSignificantGenesBarplot
                        Barplot with the number of significant genes
daUpset                 Upset plot for up- or down-regulated genes
daVis-common-args       Common parameters for the functions of the
                        'daVis' package.
daVis-common-doc        Common documentation for the 'daVis' package.
daVolcanoPlot           Volcano plot
daWaterfallPlot         Waterfall plot
downloadData            Download example data from
                        https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60450
extractColsOfInterest   Extract columns of interest from top table
extractFeatures         Extract feature ids for each overlapping set
extractPairs            Get top table per pair (ref and comp coef) for
                        scatter plot
extractQueryList        Extract query list
extractTTcoef           Extract top table for a specific coef
extractTopTables        Extract top tables for coefficients of interest
facet                   Add facets to ggplot object
filterCommonFeatures    Filter top tables based on common features
                        across all tables
filterGenesOfInterest   Filter genes of interest
filterLogFC             Filter top tables based on logFC threshold
formatAesMA             Format aesthetics for the main plot with MA
                        plot
formatAesVP             Format aesthetics for the main plot with
                        volcano plot
formatAesWP             Format aesthetics for the main plot with
                        waterfall plot
formatManualScale       extend manual scale values if required
formatTTcoef            Format top table for a specific coefficient
formatVariableLength    shorten string length
formatVariableSpace     remove space in variable name
getCoefColor            Create colors for coefficient labels
getCoefLabel            Get coefficient label
getFeatureColor         Create colors for feature labels
getFeatures             Get features from input
getInputIdCoef          Get ID of the input 'list' matching to the
                        specific coefficient
getModelCoefs           Get coefficients in input
getNumberOfRegulatedGenes
                        Get number of significant genes for coefficient
getNumberOfSignificantGenes
                        Get number of significant genes for coefficient
getSEModel              Get standard error from a limma model.
getTopFeatures          Get top features
getTopGenes             Get top genes with highest significance and top
                        genes with highest logFC
getTopTableFromModel    Extract top tables from a model
ggPlotTheme             Customized ggplot theme
isModel                 Check if input is a model
isTopTable              Check if input is a topTable containing colums
                        with logFC, p-value and adjusted p-value
labelCorr               Add label with correlation to scatter plot
labelGenesOfInterest    Add layer with genes of interest to ggplot
                        object
labelTextLRP            Add optional text to the log-ratio plot
labelTopGenes           Add point labels to ggplot object
mainH                   Create main plot object with heatmap
mainLRP                 Create main plot object with log-ratio plot
mainMA                  Create main plot object with MA plot
mainSP                  Create main plot object with scatter plot
mainVP                  Create main plot object with volcano plot
mainWP                  Create main plot object with waterfall plot
makeElementsUnique      Make elements unique
modelExampleData        Normalize data, create model matrix and
                        contrasts
orderComparison         Sort the comparison columns according to the
                        coefficients
orderFeatures           Order features based on similarity or
                        significance
processFeatures         Process table for visualizations.
reshapeTable            Reshape table
runDESeq2               Fit the model with DESeq2
runEdgeR                Fit the model with edgeR
runLimma                Fit the model with limma
runTopTable             Fit the model and return top table
setCategoricalElement   check if variable is not numeric (or integer)
setFixElement           check if the aesthetic is fixed (e.g. color,
                        shape, size 'palette')
setGradientScale        check if manual aesthetic for the gradient
                        should be set
setManualScale          check if manual aesthetic should be set
subsetFeatures          Subset input with specific features
topFeaturesDeseq        Extract top features from 'DESeq2' output
topFeaturesEdger        Extract top features from 'edgeR' output
topFeaturesLimma        Extract top features from 'limma' output
