# Generated by roxygen2: do not edit by hand

S3method(.DollarNames,AbstractTopDownSet)
S3method(all.equal,AbstractTopDownSet)
export(FragmentViews)
export(createExperimentsFragmentOptimisation)
export(createTngFusionMethFiles)
export(expandMs1Conditions)
export(expandTms2Conditions)
export(readTopDownFiles)
export(runScanHeadsman)
export(runXmlMethodChanger)
export(validMs1Settings)
export(validTms2Settings)
export(writeMethodXmls)
exportMethods("$")
exportMethods("$<-")
exportMethods("[")
exportMethods("[[")
exportMethods("[[<-")
exportMethods("colData<-")
exportMethods("conditionData<-")
exportMethods(aggregate)
exportMethods(assayData)
exportMethods(bestConditions)
exportMethods(colData)
exportMethods(combine)
exportMethods(conditionData)
exportMethods(conditionNames)
exportMethods(dim)
exportMethods(dimnames)
exportMethods(filterCv)
exportMethods(filterInjectionTime)
exportMethods(filterIntensity)
exportMethods(filterNonReplicatedFragments)
exportMethods(fragmentationMap)
exportMethods(mz)
exportMethods(normalize)
exportMethods(removeEmptyConditions)
exportMethods(rowViews)
exportMethods(show)
exportMethods(summary)
exportMethods(updateConditionNames)
exportMethods(updateMedianInjectionTime)
import(BiocGenerics)
import(Biostrings)
import(ProtGenerics)
import(S4Vectors)
import(methods)
importClassesFrom(MSnbase,MSnSet)
importClassesFrom(Matrix,Matrix)
importClassesFrom(Matrix,dgCMatrix)
importFrom(Biobase,assayData)
importFrom(IRanges,subject)
importFrom(Matrix,
  Matrix,
  crossprod,
  drop0,
  nnzero,
  sparseMatrix,
  sparseVector,
  tcrossprod
)
importFrom(PSMatch,
  calculateFragments,
  defaultNeutralLoss,
  getAminoAcids
)
importFrom(ggplot2,
  .data,
  aes,
  element_blank,
  element_line,
  element_rect,
  element_text,
  facet_grid,
  geom_hline,
  geom_segment,
  geom_text,
  geom_tile,
  geom_vline,
  ggplot,
  ggtitle,
  labs,
  scale_alpha,
  scale_color_manual,
  scale_fill_manual,
  scale_x_discrete,
  scale_y_continuous,
  theme,
  theme_classic
)
importFrom(grDevices,
  dev.off,
  pdf
)
importFrom(mzR,
  close,
  header,
  openMSfile,
  peaks,
  runInfo
)
importFrom(stats,
  ave,
  median,
  quantile,
  setNames
)
importFrom(tools,
  file_ext,
  file_path_sans_ext
)
importFrom(utils,
  .DollarNames,
  modifyList,
  object.size,
  packageVersion,
  read.csv,
  setTxtProgressBar,
  txtProgressBar
)
