Man pages for CCprofiler/CCprofiler
Complex feature detection using SEC protein chromatograms.
| annotateComplexFeatures | A helper function to extend a list of complex features with... |
| annotateMassDistribution | annotateMassDistribution |
| annotateMolecularWeight | Annotate traces with molecular weight calibration. |
| annotateTraces | Annotate traces object |
| appendSecondaryComplexFeatures | Append secondary features to scored filtered primary feature... |
| calculateCoelutionScore | Calculate coelution score for all detected features. |
| calculateFeatureCorrelation | A helper function to calculate correlation within peak... |
| calculatePathlength | Calculate pathlength from binary interactions |
| calculateQvalue | Calculate q-values from coelution score for all detected... |
| calculateSibPepCorr | calculateSibPepCorr |
| calibrateMW | calibrate Molecular Weight |
| callapseByUniqueFeatureGroups | Collapse features by unique feature groups |
| collapseComplexFeatures | Collapse detected complex fetures by common apex and... |
| collapseHypothesis | Collapse redundant hypotheses |
| complexClustering | complexClustering |
| convertIDs | Convert any input ids to uniprotkb accession ids. |
| corumComplexHypotheses | Complex hypotheses from CORUM DB |
| corumComplexHypothesesRedundant | Complex hypotheses from CORUM DB (redundant) |
| createGGplotColMap | Create a reproducible color map for a set of ids by ordering... |
| dot-collapseWideHypothesis | Collapse redundant hypotheses |
| dot-tracesTest | Test if an object is of class traces. |
| estimateComplexFeatureStoichiometry | A helper function to extend a list of complex features with... |
| estimateDecoyFDR | Estimate decoy based featureFinding FDR. |
| estimateGridSearchDecoyFDR | Estimate feature grid search FDR |
| exampleCalibrationTable | Examplary calibration table that maps molecular weights to... |
| exampleComplexFeatures | Examplary output of the 'findComplexFeatures' function |
| exampleComplexHypotheses | Example complex hypotheses |
| exampleFractionAnnotation | Examplary annotation table that maps filenames to... |
| exampleOpenSWATHinput | A sample data.table representing the output format of the... |
| examplePCPdataLong | Examplary peptide level quantitative PCP-MS dataset in long... |
| examplePCPdataWide | Examplary peptide level quantitative PCP-MS dataset in wide... |
| examplePeptideTraces | Examplary peptide level traces object before any filtering #'... |
| examplePeptideTracesFiltered | Examplary peptide level traces object after filtering |
| examplePeptideTracesUnannotated | Examplary raw peptide level traces object before any... |
| exampleProteinFeatures | Examplary output of the 'findProteinFeatures' function |
| exampleProteinTraces | Examplary protein level traces object |
| exampleTraceAnnotation | Examplary trace annotation table mapping ids in the proteomic... |
| filterByMaxCorr | Filter peptides for having at least one high correlating... |
| filterBySibPepCorr | Filter by sibling peptide correlation |
| filterByStepwiseCompleteness | Filter co-elution feature table by stepwise completeness... |
| filterConsecutiveIdStretches | Filter Consecutive Id Stretches in Chromaograms |
| filterFeatures | Filter co-elution feature table |
| filterGridSearchResults | Perform complex feature grid search filter |
| findComplexFeatures | Complex feature detection |
| findComplexFeaturesPP | A helper function to perform peak picking on the complex... |
| findComplexFeaturesSW | Detect subgroups of proteins within a matrix of protein... |
| findComplexFeaturesWithinWindow | Detect subgroups within a window. This is a helper function... |
| findFeatureBoundaries | Helper function to find boundaries of complex features. |
| findMissingValues | Find the position of missing values in a traces object |
| findProteinFeatures | Protein feature detection |
| generateBinaryNetwork | Generate a binary network from complexes. |
| generateComplexDecoys | Generate comlpex decoy-hypotheses |
| generateComplexTargets | Generate complex target-hypotheses |
| generateDecoys | Generate one comlpex decoy-hypothesis |
| generateRandomPepTraces | generateRandomPepTraces |
| getBestFeatures | Select best feature for each complex or protein id. |
| getBestParameterData | Get the best performing parameter data |
| getBestParameterStats | Get the best performing ParameterStats |
| getBestParameterStats_constraintFDR | getBestParameterStats_constraintFDR |
| getBestQvalueParameters | getBestQvalueParameters |
| getDistance | getDistance |
| getDistanceMatrix | getDistanceMatrix |
| getGenePepList | Filter peptides for having at least one high correlating... |
| getIntensityMatrix | Get intensity matrix from traces object |
| getUniqueFeatureGroups | Determine unique feature groups |
| importFromOpenSWATH | Import peptide profiles from an OpenSWATH experiment. |
| importPCPdata | Import peptide- or protein-level quantitative PCP matrix. |
| imputeMissingVals | Impute NA values in a traces object |
| imputeMissingValues | imputeMissingValues |
| imputeTraces | Plot a summary of the trace imputation |
| performComplexGridSearch | Perform complex feature grid search |
| performProteinGridSearch | Perform Protein feature grid search |
| plotComplexCompletenessScatter | Scatter plot of complex completeness |
| plotComplexMScoveragePie | plotComplexMScoveragePie. |
| plotComplexMScoverageScatter | plotComplexMScoverageScatter. |
| plotFeatures | #' #' Plot the result of the sliding window algorithm. |
| plotIdFDRspace | Plot FDR gridsearch |
| plotImputationSummary | Plot a summary of the trace imputation |
| plotProteinMScoveragePie | plotProteinMScoveragePie. |
| plotScoreDistribution | plotScoreDistribution |
| plotSibPepCorrDensities | plot SibPepCorrDensities |
| plotSummarizedComplexes | Plot pie chart with complex hypothesis completeness |
| plotSummarizedMScoverage | Plot MS coverage of the hypotheses in the PCP data |
| plot.traces | Plot traces |
| proteinQuantification | Protein Quantification |
| qvaluePositivesPlot | qvaluePositivesPlot |
| qvaluePositivesPlotGrid | qvaluePositivesPlotGrid |
| rocSibPepCorr | ROC.SibPepCorr |
| runSECexplorer | Run CCprofiler from SECexplorer y providing ids and their... |
| runSlidingWindow | runSlidingWindow function |
| scoreFeatures | Score protein or complex features and filter by q-value/FDR |
| SECexplorer_processing | SECexplorer processing. |
| subset.traces | Subset traces or fractions in traces object |
| summarizeFeatures | Summarize co-elution features |
| summarizeMassDistribution | summarizeMassDistribution |
| summary.traces | Summarize a traces object |
| toLongFormat | Convert traces from wide format to long format |
