Man pages for grandR
Comprehensive Analysis of Nucleotide Conversion Sequencing Data
| Analyses | Analysis table functions |
| AnalyzeGeneSets | Gene set analysis |
| ApplyContrasts | Apply a function over contrasts |
| as.Seurat.grandR | Create Seurat object from a grandR object |
| CalibrateEffectiveLabelingTimeKineticFit | Uses the kinetic model to calibrate the effective labeling... |
| CalibrateEffectiveLabelingTimeMatchHalflives | Calibrate the effective labeling time by matching half-lives... |
| check.analysis | Internal functions to check for a valid analysis or slot... |
| ClassifyGenes | Build the type column for the gene info table. |
| Coldata | Get the column annotation table or add additional columns to... |
| 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 |
| ComputeNtrPosteriorQuantile | 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. |
| correctdropout | Correct for 4sU dropout |
| CreateConvolutionTable | Create Convolution Table from a Seurat object |
| CreatePdfs | Convencience methods for creating QC pdfs |
| CreatePseudobulkTable | Create Pseudobulk Table from a Seurat object |
| data.apply | Internal function to apply functions to all slots etc. |
| 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 |
| dropout | Perform 4sU dropout tests |
| dropoutpercent | Estimate 4sU dropout percentages |
| estimate.dispersion | Estimate dispersion parameters for a count matrix using... |
| EstimateRegulation | Estimate regulation from snapshot experiments |
| FilterGenes | Filter genes |
| Findno4sUPairs | Find equivalent no4sU samples for 4sU samples |
| FindReferences | Obtain reference columns (samples or cells) for all columns... |
| 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... |
| FitKineticsGeneSnapshot | Compute the posterior distributions of RNA synthesis and... |
| FitKineticsPulseR | Fit kinetics using pulseR |
| FitKineticsSnapshot | Fits RNA kinetics from snapshot experiments |
| f.nonconst | Function to compute the abundance of new or old RNA at time t... |
| f.nonconst.linear | Function 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... |
| FormatCorrelation | Formatting function for correlations |
| GeneInfo | Get the gene annotation table or add additional columns to it |
| Genes | Gene and sample (or cell) names |
| GetAnalysisTable | Obtain a table of analysis results values |
| GetContrasts | Create a contrast matrix |
| GetData | Obtain a tidy table of values for a gene or a small set of... |
| GetDiagnosticParameters | Describe parameters relevant to diagnostics |
| GetMatrix | Obtain a genes x values table as a large matrix |
| get.mode.slot | Internal functions to parse mode.slot strings |
| GetPairContrasts | Create a contrast matrix for two given conditions |
| GetSignificantGenes | Significant genes |
| GetSummarizeMatrix | Create a summarize matrix |
| GetTable | Obtain a genes x values table |
| grandR | Create a grandR object and retrieve basic information |
| IsParallel | Checks for parallel execution |
| LFC | Estimation of log2 fold changes |
| LikelihoodRatioTest | Compute a likelihood ratio test. |
| ListGeneSets | List available gene sets |
| MakeColdata | Extract an annotation table from a formatted names vector |
| MAPlot | Make an MA plot |
| Normalize | Normalization |
| NormalizeBaseline | Normalization to a baseline |
| Pairwise | Log2 fold changes and Wald tests for differential expression |
| PairwiseDESeq2 | Perform Wald tests for differential expression |
| PlotAnalyses | Convenience function to make the same type of plot for... |
| PlotConversionFreq | Diagnostic plot for conversion frequencies |
| 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 |
| 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... |
| 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 |
| psapply | Parallel (s/l)apply |
| 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 |
| RotatateAxisLabels | Rotate x axis labels |
| 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... |
| SimulateReadsForSample | Simulate metabolic labeling - nucleotide conversion RNA-seq... |
| SimulateTimeCourse | Simulate a complete time course of metabolic labeling -... |
| SimulateTimeCourseNonConstant | Simulate a complete time course of metabolic labeling -... |
| Slots | Slot functions |
| structure2vector | Convert a structure into a vector |
| Summarize | Summarize a data matrix |
| ToIndex | Obtain the indices of the given genes |
| Transform.no | Transformations for PlotHeatmap |
| TransformSnapshot | Estimate parameters for a one-shot experiment. |
| UpdateSymbols | Update symbols using biomaRt |
| UseNtrSlot | Copy the NTR slot and save under new name |
| VulcanoPlot | Make a Vulcano plot |
