Function reference • MSstatsWeightedSummary

All functions

MSstatsWeightedSummary-class: Output of weighted summarization

addClusterMembership(): Add information about connected subcomponents of the peptide-protein graph to quantitative data.

adjustProteinAssignments(): Add missing proteins to PSM-level data based on a fasta database

convergenceHistory(<MSstatsWeightedSummary>): Extract convergence history from MSstatsWeightedSummary object

convergenceHistory(): Extract convergence history from MSstatsWeightedSummary object

convergenceSummary(<MSstatsWeightedSummary>): Extract convergence information from MSstatsWeightedSummary object

convergenceSummary(): Extract convergence information from MSstatsWeightedSummary object

createPeptideProteinGraph(): Wrapper around `igraph::graph_from_data_frame`

featureData(<MSstatsWeightedSummary>): Extract feature-level data from MSstatsWeightedSummary object

featureData(): Extract feature-level data from MSstatsWeightedSummary object

featureWeights(<MSstatsWeightedSummary>): Extract weights data from MSstatsWeightedSummary object

featureWeights(): Extract weights data from MSstatsWeightedSummary object

getClusterStatistics(): Calculate statistics that describe clusters of proteins and peptides.

getDiscordantInfo(): Cluster peptide profiles

getPeptideProteinWeights(): Get PSM-protein weights for summarization with shared peptides

getWeightedProteinSummary(): Get robust protein-level summary based on unique and shared peptides

getWeightsConstraints(): Get constraints for weights

makeMSstatsTMTInput(<MSstatsWeightedSummary>): Create input for MSstatsTMT::groupComparison function

makeMSstatsTMTInput(): Create input for MSstatsTMT::groupComparison function

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 without shared peptides

plotProfiles(): Plot feature profiles

plotSummary(<MSstatsWeightedSummary>): Plot summary for a given cluster or proteins set

plotSummary(): Plot summary for a given cluster or proteins set

plotSummaryComparison(): Plot multiple protein-level summaries

proteinClusters(<MSstatsWeightedSummary>): Extract cluster information from MSstatsWeightedSummary object

proteinClusters(): Extract cluster information from MSstatsWeightedSummary object

proteinData(<MSstatsWeightedSummary>): Extract protein-level data from MSstatsWeightedSummary object

proteinData(): Extract protein-level data from MSstatsWeightedSummary object

summarizeProteinsClusterSingleRun(): Optimize a given criterion to estimate protein abundances

weightsHistory(<MSstatsWeightedSummary>): Extract weights history from MSstatsWeightedSummary object

weightsHistory(): Extract weights history from MSstatsWeightedSummary object