# Comprehensive Analysis of Nucleotide Conversion Sequencing Data

## Documentation for package ‘grandR’ version 0.2.7

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

## Help Pages

A C D E F G I K L M N P R S T U V W

## -- A --

AddAnalysis | Analysis table functions
AddGenePlot | Stored plot functions
AddGlobalPlot | Stored plot functions
AddSlot | Slot functions
Analyses | Analysis table functions
AnalyzeGeneSets | Gene set analysis
ApplyContrasts | Apply a function over contrasts
as.Seurat.grandR | Create Seurat object from a grandR object

## -- C --

CalibrateEffectiveLabelingTimeKineticFit | Uses the kinetic model to calibrate the effective labeling time.
CalibrateEffectiveLabelingTimeMatchHalflives | Calibrate the effective labeling time by matching half-lives to a .reference
check.analysis | Internal functions to check for a valid analysis or slot names.
check.mode.slot | Internal functions to check for a valid analysis or slot names.
check.slot | Internal functions to check for a valid analysis or slot names.
ClassifyGenes | Build the type column for the gene info table.
Coldata | Get the column annotation table or add additional columns to it
Coldata<- | Get the column annotation table or add additional columns to it
Columns | Gene and sample (or cell) names
ComputeColumnStatistics | Compute statistics for all columns (i.e. samples or cells)
ComputeExpressionPercentage | Expression percentage computation
ComputeNonConstantParam | Compute and evaluate functions for non constant rates
ComputeNtrCI | Compute NTR quantiles
ComputeNtrPosteriorLower | Compute NTR quantiles
ComputeNtrPosteriorQuantile | Compute NTR quantiles
ComputeNtrPosteriorUpper | Compute NTR quantiles
ComputePseudoNtr | Compute pseudo NTRs from two count matrices
ComputeSteadyStateHalfLives | Steady state half-lives for each sample
ComputeSummaryStatistics | Compute summary statistics
ComputeTotalExpression | Total expression computation
Condition | Get or set the conditions in the column annotation table.
Condition<- | Get or set the conditions in the column annotation table.
Correct4sUDropoutHLFactor | Correct for 4sU dropout
Correct4sUDropoutHLSpline | Correct for 4sU dropout
correctdropout | Correct for 4sU dropout
CreateConvolutionTable | Create Convolution Table from a Seurat object
CreatePdfs | Convencience methods for creating QC pdfs
CreatePdfsComparison | Convencience methods for creating QC pdfs
CreatePdfsParameters | Convencience methods for creating QC pdfs
CreatePdfsProfiles | Convencience methods for creating QC pdfs
CreatePseudobulkTable | Create Pseudobulk Table from a Seurat object

## -- D --

data.apply | Internal function to apply functions to all slots etc.
DefaultSlot | Get or set the default slot for a grandR object.
DefaultSlot<- | Get or set the default slot for a grandR object.
Defer | Defer calling a function
density2d | Density estimation in 2d
DESeq2BIC | Compute the Bayesian information criterion (BIC)
Design | A list of predefined names for design vectors
DesignSemantics | Build the design semantics list
dim.grandR | Create a grandR object and retrieve basic information
dimnames.grandR | Create a grandR object and retrieve basic information
DropAnalysis | Analysis table functions
dropout | Perform 4sU dropout tests
dropoutpercent | Estimate 4sU dropout percentages
DropPlots | Stored plot functions
DropSlot | Slot functions

## -- E --

estimate.dispersion | Estimate dispersion parameters for a count matrix using DESeq2
Estimate4sUDropoutPercentage | Estimate 4sU dropout percentages
Estimate4sUDropoutPercentageForSample | Estimate 4sU dropout percentages
EstimateRegulation | Estimate regulation from snapshot experiments
EvaluateNonConstantParam | Compute and evaluate functions for non constant rates

## -- F --

f.new | Functions to compute the abundance of new or old RNA at time t.
f.nonconst | Function to compute the abundance of new or old RNA at time t for non-constant rates.
f.nonconst.linear | Function to compute the abundance of new or old RNA at time t for non-constant rates.
f.old.equi | Functions to compute the abundance of new or old RNA at time t.
f.old.nonequi | Functions to compute the abundance of new or old RNA at time t.
FilterGenes | Filter genes
Findno4sUPairs | Find equivalent no4sU samples for 4sU samples
FindReferences | Obtain reference columns (samples or cells) for all columns (samples or cells) in the data set
FitKinetics | Fit kinetic models to all genes.
FitKineticsGeneLeastSquares | Fit a kinetic model according to non-linear least squares.
FitKineticsGeneLogSpaceLinear | Fit a kinetic model using a linear model.
FitKineticsGeneNtr | Fit a kinetic model using the degradation rate transformed NTR posterior distribution.
FitKineticsGeneSnapshot | Compute the posterior distributions of RNA synthesis and degradation for a particular gene
FitKineticsPulseR | Fit kinetics using pulseR
FitKineticsSnapshot | Fits RNA kinetics from snapshot experiments
FormatCorrelation | Formatting function for correlations

## -- G --

GeneInfo | Get the gene annotation table or add additional columns to it
GeneInfo<- | Get the gene annotation table or add additional columns to it
Genes | Gene and sample (or cell) names
get.mode.slot | Internal functions to parse mode.slot strings
GetAnalysisTable | Obtain a table of analysis results values
GetContrasts | Create a contrast matrix
GetContrasts.default | Create a contrast matrix
GetContrasts.grandR | Create a contrast matrix
GetData | Obtain a tidy table of values for a gene or a small set of genes
GetDiagnosticParameters | Describe parameters relevant to diagnostics
GetMatrix | Obtain a genes x values table as a large matrix
GetPairContrasts | Create a contrast matrix for two given conditions
GetSignificantGenes | Significant genes
GetSummarizeMatrix | Create a summarize matrix
GetSummarizeMatrix.default | Create a summarize matrix
GetSummarizeMatrix.grandR | Create a summarize matrix
GetTable | Obtain a genes x values table
grandR | Create a grandR object and retrieve basic information

## -- I --

is.grandR | Create a grandR object and retrieve basic information
IsParallel | Checks for parallel execution
IsSparse | Create a grandR object and retrieve basic information

## -- K --

kinetics2vector | Convert a structure into a vector

## -- L --

LFC | Estimation of log2 fold changes
LikelihoodRatioTest | Compute a likelihood ratio test.
ListGeneSets | List available gene sets

## -- M --

MakeColdata | Extract an annotation table from a formatted names vector
MAPlot | Make an MA plot
merge.grandR | Create a grandR object and retrieve basic information
Metadata | Create a grandR object and retrieve basic information

## -- N --

Normalize | Normalization
NormalizeBaseline | Normalization to a baseline
NormalizeFPKM | Normalization
NormalizeRPM | Normalization
NormalizeTPM | Normalization

## -- P --

Pairwise | Log2 fold changes and Wald tests for differential expression
PairwiseDESeq2 | Perform Wald tests for differential expression
plapply | Parallel (s/l)apply
Plot4sUDropout | Perform 4sU dropout tests
Plot4sUDropoutAll | Perform 4sU dropout tests
Plot4sUDropoutDeferAll | Perform 4sU dropout tests
Plot4sUDropoutRank | Perform 4sU dropout tests
Plot4sUDropoutRankAll | Perform 4sU dropout tests
Plot4sUDropoutRankDeferAll | Perform 4sU dropout tests
PlotAnalyses | Convenience function to make the same type of plot for multple analyses.
PlotConversionFreq | Diagnostic plot for conversion frequencies
PlotGene | Stored plot functions
PlotGeneGroupsBars | Plot gene values as bars
PlotGeneGroupsPoints | Plot gene groups as points
PlotGeneOldVsNew | Gene plot comparing old vs new RNA
PlotGeneProgressiveTimecourse | Plot progressive labeling timecourses
PlotGeneSnapshotTimecourse | Gene plot for snapshot timecourse data
PlotGeneTotalVsNtr | Gene plot comparing total RNA vs the NTR
PlotGlobal | Stored plot functions
PlotHeatmap | Create heatmaps from grandR objects
PlotMismatchPositionForSample | Diagnostic plot for mismatch position for columns (by sample)
PlotMismatchPositionForType | Diagnostic plot for mismatch position for columns (by mismatch type)
PlotModelCompareConv | Diagnostic plot for estimated models (global conversion rate)
PlotModelCompareErr | Diagnostic plot for estimated models (global error rate)
PlotModelCompareErrPrior | Diagnostic plot for estimated models (global error rate)
PlotModelCompareLL | Diagnostic plot for estimated models (log likelihoods)
PlotModelCompareNtr | Diagnostic plot for estimated models (global NTR)
PlotModelConv | Diagnostic plot for estimated models (global conversion rate)
PlotModelErr | Diagnostic plot for estimated models (global error rate)
PlotModelLabelTimeCourse | Diagnostic plot for estimated models (4sU increase)
PlotModelNtr | Diagnostic plot for estimated models (global NTR)
PlotModelShape | Diagnostic plot for estimated models (global shape parameter)
PlotPCA | Make a PCA plot
PlotProfileLikelihood | Diagnostic plot for estimated models (global error rate)
Plots | Stored plot functions
PlotScatter | Make a scatter plot
PlotSimulation | Plot simulated data
PlotTypeDistribution | Plot the distribution of gene types
PoolColumns | Pool reads across columns
print.grandR | Create a grandR object and retrieve basic information
psapply | Parallel (s/l)apply

## -- R --

ReadCounts | Read a count table
ReadFeatureCounts | Read featureCounts
ReadGRAND | Read the output of GRAND-SLAM 2.0 into a grandR object.
ReadGRAND3 | Read the output of GRAND-SLAM 3.0 into a grandR object.
ReadNewTotal | Read sparse new/total matrices
RenameColumns | Create a grandR object and retrieve basic information
Renamer | Create a renamer function
RotatateAxisLabels | Rotate x axis labels

## -- S --

SaveNtrSlot | Copy the NTR slot and save under new name
Scale | Scale data
Semantics.concentration | Semantics for concentration columns
Semantics.time | Semantics for time columns
ServeGrandR | Serve a shiny web interface
SetParallel | Set up parallel execution
SimulateKinetics | Simulate the kinetics of old and new RNA for given parameters.
SimulateReadsForSample | Simulate metabolic labeling - nucleotide conversion RNA-seq data.
SimulateTimeCourse | Simulate a complete time course of metabolic labeling - nucleotide conversion RNA-seq data.
SimulateTimeCourseNonConstant | Simulate a complete time course of metabolic labeling - nucleotide conversion RNA-seq data.
Slots | Slot functions
split.grandR | Create a grandR object and retrieve basic information
structure2vector | Convert a structure into a vector
subset.grandR | Create a grandR object and retrieve basic information
Summarize | Summarize a data matrix
SwapColumns | Create a grandR object and retrieve basic information

## -- T --

Title | Create a grandR object and retrieve basic information
ToIndex | Obtain the indices of the given genes
Transform.logFC | Transformations for PlotHeatmap
Transform.no | Transformations for PlotHeatmap
Transform.VST | Transformations for PlotHeatmap
Transform.Z | Transformations for PlotHeatmap
TransformSnapshot | Estimate parameters for a one-shot experiment.

## -- U --

UpdateSymbols | Update symbols using biomaRt
UseNtrSlot | Use the given slot as NTR (is overwritten!)

## -- V --

VulcanoPlot | Make a Vulcano plot

## -- W --

Wilcoxon | Perform Wilcoxon tests for differential expression