# Generated by roxygen2: do not edit by hand

export("reduced<-")
export(ConnectedComponents)
export(PSM)
export(addFragments)
export(ccMatrix)
export(connectedComponents)
export(defaultNeutralLoss)
export(describePeptides)
export(describeProteins)
export(filterPSMs)
export(filterPsmDecoy)
export(filterPsmFdr)
export(filterPsmRank)
export(filterPsmShared)
export(getAminoAcids)
export(getAtomicMass)
export(makeAdjacencyMatrix)
export(makePeptideProteinVector)
export(plotAdjacencyMatrix)
export(prioritiseConnectedComponents)
export(prioritizeConnectedComponents)
export(psmVariables)
export(readPSMs)
export(reducePSMs)
export(reduced)
exportClasses(PSM)
exportMethods("[")
exportMethods(adjacencyMatrix)
exportMethods(calculateFragments)
exportMethods(dims)
exportMethods(length)
exportMethods(ncols)
exportMethods(nrows)
import(BiocParallel)
import(S4Vectors)
importClassesFrom(S4Vectors,DFrame)
importClassesFrom(S4Vectors,DataFrame)
importFrom(BiocGenerics,dims)
importFrom(BiocGenerics,fileName)
importFrom(BiocGenerics,ncols)
importFrom(BiocGenerics,nrows)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(Matrix,tcrossprod)
importFrom(MsCoreUtils,common)
importFrom(ProtGenerics,adjacencyMatrix)
importFrom(ProtGenerics,calculateFragments)
importFrom(QFeatures,reduceDataFrame)
importFrom(igraph,"V<-")
importFrom(igraph,V)
importFrom(igraph,cluster_louvain)
importFrom(igraph,components)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_incidence_matrix)
importFrom(igraph,groups)
importFrom(igraph,layout_nicely)
importFrom(igraph,modularity)
importFrom(igraph,plot.igraph)
importFrom(igraph,set_vertex_attr)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(stats,setNames)
importFrom(utils,adist)
