Man pages for jweile/tileseqMave
TileSeq MAVE Analysis pipeline
| adhocLogPhiSD | Helper function to calculate ad-hoc log(phi) replicate stdev... |
| adjustTableDepth | Adjust dataframe 'covTable' with mean "effective" sequencing... |
| analyzeComplexity | Determine complexity of all varinats in allCounts; look at... |
| analyzeLegacyTileseqCounts | analyze tileseq counts from legacy pipeline |
| biasCorrection | Run read-frequecy bias correction on logPhi |
| bnl | Baldi & Long's formula |
| buildJointTable | run library quality control (QC) |
| buildPlotMatrix | Helper function to build layout for coverage map |
| buildSimplifiedMarginal | Build a simplified version of the marginal table with columns... |
| calcDepthDrops | Calculate relative drops in effective sequencing depth for... |
| calcEnrichment | calculate logPhi enrichment ratios |
| calcPhi | Calculate enrichment ratios (phi) and perform error... |
| calculateFits | Calculate lambda and Poisson fits for each census |
| charProfile | Get a contingency table of characters in a file |
| checkCSV | Checks if a file is a CSV file or throws errors |
| codonAgreement | Draw plots to analyze agreement between equivalent codons |
| collapseByAA | Collapse score table by amino acid changes |
| countAttributes | Output alignment quality plot with percentages of unmapped or... |
| coverageSubmap | Helper function to draw a subsection of the coverage map |
| csvParam2Json | convert CSV input parameter file to JSON format |
| dot-onAttach | Show message at startup |
| drawComplexity | Output complexity plot with the marginal frequency of... |
| drawCoverageLegend | Draw legend for coverage maps |
| drawCoverageMap | Output heatmap of marginal frequencies for all possible amino... |
| drawDistributions | Delegation function to draw score distribution plots with a... |
| drawNucleotideBias | Draw Nucleotide Bias Analysis plots |
| drawPositionalDepth | Output effective depth plot with effective sequencing depth... |
| dropoutAnalysis | run variant dropout troubleshooter |
| enactScale | Calculate scores by scaling logPhi (or bce values, as... |
| errorProfile | Draw error profile for the dataset |
| expectedError | Infer a function that models expected error relative to data... |
| exportExperiment | Export simulated experiment |
| exportRawAssay | Exports raw assay data |
| exportSeqSample | Export count data to file |
| filterProgression | Draw replicate correlation plots |
| filterVariants | Filter variants that have greater depth drop than max allowed... |
| findQuads | Helper function to find the quad of conditions and time... |
| findRuns | Finds runs of TRUE values in a boolean vector |
| fit.cv.model | Create a model of the error in for a subset of marginal... |
| floor0 | Helper function to bottom-out a vector of numbers, so that no... |
| flooring | Apply flooring and SD adjustment to negative scores |
| fluorScore | score fluorescence data |
| getNonselectFor | Convenience function get the matching non-selective condition... |
| getNonselects | Convenience function get all non-selective conditions |
| getNsConditions | Get all nonselect conditions from parameter sheet object |
| getPivotOverrides | Helper function to extract scaling pivot point override... |
| getSelects | Convenience function get all selective conditions |
| getTimepointsFor | Convenience function get the available time points for the... |
| getWTControlFor | Convenience function get the matching WT control condition... |
| getWTReps | Extract appropriate WT replicates for timepoint given in... |
| inferTiles | Determine which tiles the positions from split codon changes... |
| join.datapoints | join multiple datapoints weighted by stdev |
| joinRawInputs | join raw input datasets |
| latestSubDir | Convenience function to find a subdirectory matching the... |
| legacyCountConverter | converts legacy tileseq count data into the new count file... |
| libraryQC | run library quality control (QC) |
| libraryQCLegacy | QC plots for library coverage |
| logInfo | convenience logging function at INFO level |
| logPhiBias | Plot the logPhi bias vs the nonselect marginal frequency |
| log.sd | Error propagation formula for the logarithm of a Random... |
| logVersion | Convenience function for recording the package version into... |
| logWarn | convenience logging function at WARN level |
| mavedbCountExport | Convert count files from legacy pipeline to MaveDB format |
| mean.sd.count | Function to form mean, stdev and average raw count for a... |
| mut_breakdown | Return the sums of marginal frequencies for different types... |
| nucleotideBiasAnalysis | Helper function to perform nucleotide bias analysis and draw... |
| parseCountFile | parse a count table |
| parseCoverageFile | parse coverage data file |
| parseParameters | parse JSON parameter file |
| pdftagger | Helper object for adding tags to pdf page margins |
| plotCensus | Helper function to plot a census dataset |
| plotCoverageCurve | Output coverage curves showing the progression of how many... |
| plotDepthDrops | Output depth drop distribution plot showing distribution of... |
| plotFrameshiftHotspot | Output frameshift hotspot plot with distribution of... |
| plotJackpotDiagnosis | Output jackpot plot with marginal frequencies of all variants... |
| plotMutbreakdown | Output variant-type breakdown for each tile |
| plotReplicateCorrelation | Output replicate correlation plot between technical... |
| plotSeqErrorRates | Output basecall quality plot with observed error rate at... |
| plotWTCtrl | Draw WT frequency plot comparing distribution of marginal... |
| ratio.sd | Error propagation formula for ratios of Random Variables |
| rawFilter | Function to apply filtering based on raw counts / frequency |
| reachableChanges | Convenience function to calculate the list of SNV-reachable... |
| regionCensus | Perform census on overall region to determine what mutations... |
| registerLogger | Globally registers a logger object |
| regularizationQC | Draw error regulariztion model QC plots |
| regularizeRaw | Function to perform Baldi & Long's error regularization |
| replicateCorrelation | Draw replicate correlation plots |
| residualError | Calculate the residual error |
| runModelFits | Run model fitting on all tiles in all given conditions |
| scaleScores | perform scaling of logPhi into final scores |
| scoreDistributions | Draw score distribution plots |
| selectionQC | run library quality control (QC) |
| simulateAssay | Simulate selection assay |
| simulateExperiment | Title |
| simulateFitness | Simulate Clone fitness |
| simulatePool | Simulate Pool |
| simulateTileSeq | simulate TileSeq |
| slide | Underlying function for error profile model |
| splitCodonChanges | Extract affected positions and codon details from vector... |
| startupMessage | Generates the the startup message |
| synNonDelta | Draws a plot showing running means of synonymous and nonsense... |
| tileCensus | Perform census on tile to determine what mutations are... |
| tilesInRegions | Convenience function to find the tiles that belong to each... |
| validateParameters | run validation checks on parameters object |
