# Generated by roxygen2: do not edit by hand

S3method(.DollarNames,AbstractTopDownSet)
S3method(all,equal.AbstractTopDownSet)
export(FragmentViews)
export(createExperimentsFragmentOptimisation)
export(createTngFusionMethFiles)
export(defaultMs1Settings)
export(defaultMs2Settings)
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(MSnbase,calculateFragments)
importFrom(MSnbase,defaultNeutralLoss)
importFrom(MSnbase,get.amino.acids)
importFrom(Matrix,Matrix)
importFrom(Matrix,crossprod)
importFrom(Matrix,drop0)
importFrom(Matrix,nnzero)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,sparseVector)
importFrom(Matrix,tcrossprod)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(mzR,close)
importFrom(mzR,header)
importFrom(mzR,openMSfile)
importFrom(mzR,peaks)
importFrom(mzR,runInfo)
importFrom(stats,ave)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(utils,.DollarNames)
importFrom(utils,modifyList)
importFrom(utils,object.size)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
