Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Documentation for package ‘grandR’ version 0.2.5

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-- 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
ComputeAbsolute	Compute absolute expression using ERCC spike ins
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
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
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
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	Copy the NTR slot and save under new name

-- V --

VulcanoPlot

Make a Vulcano plot