
Function reference
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ClassifyGenes()
- Build the type column for the gene info table.
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Design
- A list of predefined names for design vectors
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DesignSemantics()
- Build the design semantics list
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MakeColdata()
- Extract an annotation table from a formatted names vector
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ReadGRAND()
- Read the output of GRAND-SLAM 2.0 into a grandR object.
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ReadGRAND3()
- Read the output of GRAND-SLAM 3.0 into a grandR object.
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Semantics.time()
- Semantics for time columns
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ComputeAbsolute()
- Compute absolute expression using ERCC spike ins
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ComputeNtrPosteriorQuantile()
ComputeNtrCI()
ComputeNtrPosteriorLower()
ComputeNtrPosteriorUpper()
- Compute NTR quantiles
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FilterGenes()
- Filter genes
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Normalize()
NormalizeFPKM()
NormalizeRPM()
NormalizeTPM()
- Normalization
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NormalizeBaseline()
- Normalization to a baseline
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Scale()
- Scale data
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Analyses()
AddAnalysis()
DropAnalysis()
- Analysis table functions
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Coldata()
`Coldata<-`()
- Get the column annotation table or add additional columns to it
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Condition()
`Condition<-`()
- Get or set the conditions in the column annotation table.
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DefaultSlot()
`DefaultSlot<-`()
- Get or set the default slot for a grandR object.
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GeneInfo()
`GeneInfo<-`()
- Get the gene annotation table or add additional columns to it
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Plots()
AddGenePlot()
AddGlobalPlot()
PlotGene()
PlotGlobal()
DropPlots()
- Stored plot functions
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Slots()
DropSlot()
AddSlot()
- Slot functions
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grandR()
VersionString()
Title()
dim(<grandR>)
is.grandR()
dimnames(<grandR>)
print(<grandR>)
subset(<grandR>)
split(<grandR>)
merge(<grandR>)
- Create a grandR object and retrieve basic information
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ComputeExpressionPercentage()
- Expression percentage computation
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GetAnalysisTable()
- Obtain a table of analysis results values
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GetData()
- Obtain a tidy table of values for a gene or a small set of genes
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GetSparseMatrix()
- Obtain a genes x values table as a sparse matrix
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GetSummarizeMatrix()
- Create a summarize matrix
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GetTable()
- Obtain a genes x values table
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EstimateRegulation()
- Estimate regulation from snapshot experiments
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GetContrasts()
- Create a contrast matrix
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GetSignificantGenes()
- Significant genes
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LFC()
- Estimation of log2 fold changes
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LikelihoodRatioTest()
- Compute a likelihood ratio test.
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PairwiseDESeq2()
- Perform Wald tests for differential expression
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FitKinetics()
- Fit kinetic models to all genes.
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FitKineticsGeneLeastSquares()
- Fit a kinetic model according to non-linear least squares.
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FitKineticsGeneLogSpaceLinear()
- Fit a kinetic model using a linear model.
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FitKineticsGeneNtr()
- Fit a kinetic model using the degradation rate transformed NTR posterior distribution.
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FitKineticsPulseR()
- Fit kinetics using pulseR
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PlotSimulation()
- Plot simulated data
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SimulateKinetics()
- Simulate the kinetics of old and new RNA for given parameters.
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f.old.equi()
f.old.nonequi()
f.new()
- Functions to compute the abundance of new or old RNA at time t.
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ComputeSteadyStateHalfLives()
- Steady state half-lives for each sample
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FindReferences()
- Obtain reference columns (samples or cells) for all columns (samples or cells) in the data set
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FitKineticsGeneSnapshot()
- Compute the posterior distributions of RNA synthesis and degradation for a particular gene
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FitKineticsSnapshot()
- Fits RNA kinetics from snapshot experiments
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TransformSnapshot()
- Estimate parameters for a one-shot experiment.
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AnalyzeGeneSets()
- Gene set analysis
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ListGeneSets()
- List available gene sets
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PlotGeneGroupsBars()
- Plot gene values as bars
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PlotGeneGroupsPoints()
- Plot gene groups as points
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PlotGeneOldVsNew()
- Gene plot comparing old vs new RNA
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PlotGeneProgressiveTimecourse()
- Plot progressive labeling timecourses
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PlotGeneSnapshotTimecourse()
- Gene plot for snapshot timecourse data
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PlotGeneTotalVsNtr()
- Gene plot comparing total RNA vs the NTR
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FormatCorrelation()
- Formatting function for correlations
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MAPlot()
- Make an MA plot
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PlotAnalyses()
- Convenience function to make the same type of plot for multple analyses.
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PlotHeatmap()
- Create heatmaps from grandR objects
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PlotPCA()
- Make a PCA plot
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PlotScatter()
- Make a scatter plot
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PlotTypeDistribution()
- Plot the distribution of gene types
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Transform.no()
Transform.Z()
Transform.VST()
Transform.logFC()
- Transformations for PlotHeatmap
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VulcanoPlot()
- Make a Vulcano plot
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ServeGrandR()
- Serve a shiny web interface
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Findno4sUPairs()
- Find equivalent no4sU samples for 4sU samples
Temporal recalibration
Functions for recalibration of labeling times (to get effective labeling from nominal labeling times)
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CalibrateEffectiveLabelingTimeKineticFit()
- Uses the kinetic model to calibrate the effective labeling time.
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CalibrateEffectiveLabelingTimeMatchHalflives()
- Calibrate the effective labeling time by matching half-lives to a .reference
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GetDiagnosticParameters()
- Describe parameters relevant to diagnostics
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PlotConversionFreq()
- Diagnostic plot for conversion frequencies
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PlotMismatchPositionForSample()
- Diagnostic plot for mismatch position for columns (by sample)
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PlotMismatchPositionForType()
- Diagnostic plot for mismatch position for columns (by mismatch type)
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PlotModelCompareConv()
- Diagnostic plot for estimated models (global conversion rate)
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PlotModelCompareErr()
- Diagnostic plot for estimated models (global error rate)
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PlotModelCompareErrPrior()
- Diagnostic plot for estimated models (global error rate)
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PlotModelCompareLL()
- Diagnostic plot for estimated models (log likelihoods)
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PlotModelCompareNtr()
- Diagnostic plot for estimated models (global NTR)
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PlotModelConv()
- Diagnostic plot for estimated models (global conversion rate)
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PlotModelErr()
- Diagnostic plot for estimated models (global error rate)
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PlotModelLabelTimeCourse()
- Diagnostic plot for estimated models (4sU increase)
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PlotModelNtr()
- Diagnostic plot for estimated models (global NTR)
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PlotModelShape()
- Diagnostic plot for estimated models (global shape parameter)
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PlotProfileLikelihood()
- Diagnostic plot for estimated models (global error rate)
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SimulateReadsForSample()
- Simulate metabolic labeling - nucleotide conversion RNA-seq data.
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SimulateTimeCourse()
- Simulate a complete time course of metabolic labeling - nucleotide conversion RNA-seq data.
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ApplyContrasts()
- Apply a function over contrasts
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Defer()
- Defer calling a function
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IsParallel()
- Checks for parallel execution
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RotatateAxisLabels()
- Rotate x axis labels
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SetParallel()
- Set up parallel execution
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ToIndex()
- Obtain the indices of the given genes
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check.analysis()
check.slot()
check.mode.slot()
- Internal functions to check for a valid analysis or slot names.
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data.apply()
- Internal function to apply functions to all slots etc.
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density2d()
- Density estimation in 2d
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estimate.dispersion()
- Estimate dispersion parameters for a count matrix using DESeq2
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get.mode.slot()
- Internal functions to parse mode.slot strings
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structure2vector()
kinetics2vector()
- Convert a structure into a vector