Comprehensive Analysis of Nucleotide Conversion Sequencing Data


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Documentation for package ‘grandR’ version 0.2.0

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

-- 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

-- 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
ComputeExpressionPercentage Expression percentage computation
ComputeNtrCI Compute NTR quantiles
ComputeNtrPosteriorLower Compute NTR quantiles
ComputeNtrPosteriorQuantile Compute NTR quantiles
ComputeNtrPosteriorUpper Compute NTR quantiles
ComputeSteadyStateHalfLives Steady state half-lives for each sample
Condition Get or set the conditions in the column annotation table.
Condition<- Get or set the conditions in the column annotation table.

-- 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
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
DropPlots Stored plot functions
DropSlot Slot functions

-- E --

estimate.dispersion Estimate dispersion parameters for a count matrix using DESeq2
EstimateRegulation Estimate regulation from snapshot experiments

-- F --

f.new Functions to compute the abundance of new or old RNA at time t.
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
GetSignificantGenes Significant genes
GetSparseMatrix Obtain a genes x values table as a sparse matrix
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

-- 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

-- N --

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

-- P --

PairwiseDESeq2 Perform Wald tests for differential expression
plapply Parallel (s/l)apply
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
PlotToxicityTest Perform toxicity tests
PlotToxicityTestAll Perform toxicity tests
PlotToxicityTestDeferAll Perform toxicity tests
PlotToxicityTestRank Perform toxicity tests
PlotToxicityTestRankAll Perform toxicity tests
PlotToxicityTestRankDeferAll Perform toxicity tests
PlotTypeDistribution Plot the distribution of gene types
print.grandR Create a grandR object and retrieve basic information
psapply Parallel (s/l)apply

-- R --

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.
RotatateAxisLabels Rotate x axis labels

-- S --

Scale Scale data
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.
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

-- T --

Title Create a grandR object and retrieve basic information
ToIndex Obtain the indices of the given genes
toxicity Perform toxicity tests
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.

-- V --

VersionString Create a grandR object and retrieve basic information
VulcanoPlot Make a Vulcano plot