# Generated by roxygen2: do not edit by hand

export("reduced<-")
export(ConnectedComponents)
export(PSM)
export(ccMatrix)
export(checkABpresence)
export(checkOverlap)
export(checkParentIonIntensity)
export(checkPrecursorPurity)
export(checkShiftConsistency)
export(checkXYpresence)
export(connectedComponents)
export(defaultNeutralLoss)
export(describePeptides)
export(describeProteins)
export(filterPSMs)
export(filterPsmDecoy)
export(filterPsmFdr)
export(filterPsmRank)
export(filterPsmShared)
export(getAminoAcids)
export(getAtomicMass)
export(labelFragments)
export(makeAdjacencyMatrix)
export(makePeptideProteinVector)
export(plotAdjacencyMatrix)
export(plotSpectraPTM)
export(prioritiseConnectedComponents)
export(prioritizeConnectedComponents)
export(psmVariables)
export(readPSMs)
export(reducePSMs)
export(reduced)
export(validatePSM)
exportClasses(PSM)
exportMethods("[")
exportMethods(adjacencyMatrix)
exportMethods(calculateFragments)
exportMethods(dims)
exportMethods(length)
exportMethods(ncols)
exportMethods(nrows)
import(BiocParallel)
import(PTMods)
import(S4Vectors)
importClassesFrom(S4Vectors,DFrame)
importClassesFrom(S4Vectors,DataFrame)
importFrom(BiocGenerics,
  dims,
  fileName,
  ncols,
  nrows
)
importFrom(Matrix,
  Matrix,
  colSums,
  rowSums,
  sparseMatrix,
  t,
  tcrossprod
)
importFrom(MsCoreUtils,closest)
importFrom(ProtGenerics,
  adjacencyMatrix,
  calculateFragments
)
importFrom(QFeatures,reduceDataFrame)
importFrom(Spectra,
  peaksData,
  precursorCharge,
  precursorPurity,
  spectraData,
  spectraVariables
)
importFrom(grDevices,
  n2mfrow,
  xy.coords
)
importFrom(graphics,
  abline,
  axis,
  layout,
  mtext,
  par,
  plot.new,
  plot.window,
  plot.xy,
  points,
  segments,
  strheight,
  strwidth,
  text,
  title
)
importFrom(igraph,
  "V<-",
  V,
  cluster_louvain,
  components,
  graph_from_adjacency_matrix,
  graph_from_biadjacency_matrix,
  groups,
  layout_nicely,
  modularity,
  plot.igraph,
  set_vertex_attr
)
importFrom(methods,
  as,
  is,
  new
)
importFrom(stats,setNames)
importFrom(utils,adist)
