Man pages for Vitek-Lab/SharedPeptidesExplorer
Weighted Protein-Level Summarization for Protein Clusters
| addClusterMembership | Add information about connected subcomponents of the... |
| adjustProteinAssignments | Add missing proteins to PSM-level data based on a fasta... |
| checkDataCorrectness | Check if data is in MSstatsTMT format |
| convergenceHistory | Extract convergence history from MSstatsWeightedSummary... |
| convergenceHistory-MSstatsWeightedSummary-method | Extract convergence history from MSstatsWeightedSummary... |
| convergenceSummary | Extract convergence information from MSstatsWeightedSummary... |
| convergenceSummary-MSstatsWeightedSummary-method | Extract convergence information from MSstatsWeightedSummary... |
| createPeptideProteinGraph | Wrapper around 'igraph::graph_from_data_frame' |
| featureData | Extract feature-level data from MSstatsWeightedSummary object |
| featureData-MSstatsWeightedSummary-method | Extract feature-level data from MSstatsWeightedSummary object |
| featureWeights | Extract weights data from MSstatsWeightedSummary object |
| featureWeights-MSstatsWeightedSummary-method | Extract weights data from MSstatsWeightedSummary object |
| getAnnotation | Make annotation |
| getClusterStatistics | Calculate statistics that describe clusters of proteins and... |
| getClusterSummaries | Calculate weighted summaries for a list of clusters |
| getConvergenceHistory | Get details of convergence |
| getConvergenceSummary | Get convergence summary |
| getCurrentWeights | Utility function to get weights from current iterations... |
| getDiscordantInfo | Cluster peptide profiles |
| getPeptideProteinWeights | Get PSM-protein weights for summarization with shared... |
| getProteinsClusters | Split data into a list of clusters |
| getProteinsOptimProblem | Get optimization problem for protein-level summaries |
| getProteinSummaryDesign | Get design matrix for protein-level summarization |
| getWeightedProteinSummary | Get robust protein-level summary based on unique and shared... |
| getWeightedSummarySingleRun | Robust summary for a single run |
| getWeightsConstraints | Get constraints for weights |
| getWeightsDesign | Get design matrix and response for weights calculation |
| getWeightsHistory | Get history of weights from all iterations |
| getWeightsSummary | Get summary of final weights |
| makeMSstatsTMTInput | Create input for MSstatsTMT::groupComparison function |
| makeMSstatsTMTInput-MSstatsWeightedSummary-method | Create input for MSstatsTMT::groupComparison function |
| MSstatsWeightedSummary-class | Output of weighted summarization |
| normalizePeptides | Normalization between channels (before summarization) |
| normalizeSharedPeptides | Normalization for TMT data with shared peptides |
| plotClusterStats | Plot statistics about clusters of proteins |
| plotDistributionComparison | Compare distribution of log2-intensities per channel with and... |
| plotProfiles | Plot feature profiles |
| plotSummary | Plot summary for a given cluster or proteins set |
| plotSummaryComparison | Plot multiple protein-level summaries |
| plotSummary-MSstatsWeightedSummary-method | Plot summary for a given cluster or proteins set |
| processProteinOptimSolution | Get protein abundances from optimization result |
| processSummarizationOutput | Prepare summarizaton output |
| proteinClusters | Extract cluster information from MSstatsWeightedSummary... |
| proteinClusters-MSstatsWeightedSummary-method | Extract cluster information from MSstatsWeightedSummary... |
| proteinData | Extract protein-level data from MSstatsWeightedSummary object |
| proteinData-MSstatsWeightedSummary-method | Extract protein-level data from MSstatsWeightedSummary object |
| summarizeProteinsClusterSingleRun | Optimize a given criterion to estimate protein abundances |
| weightsHistory | Extract weights history from MSstatsWeightedSummary object |
| weightsHistory-MSstatsWeightedSummary-method | Extract weights history from MSstatsWeightedSummary object |
