topdownr-package	topdownr-package
$,AbstractTopDownSet-method	AbstractTopDownSet-class
$<-,AbstractTopDownSet-method	AbstractTopDownSet-class
AbstractTopDownSet-class	AbstractTopDownSet-class
aggregate,TopDownSet-method	TopDownSet-class
assayData,AbstractTopDownSet-method	AbstractTopDownSet-class
bestConditions	NCBSet-class
bestConditions,NCBSet-method	NCBSet-class
coerce,FragmentViews,data.frame-method	FragmentViews-class
coerce,TopDownSet,MSnSet-method	TopDownSet-class
coerce,TopDownSet,NCBSet-method	TopDownSet-class
colData	AbstractTopDownSet-class
colData,AbstractTopDownSet-method	AbstractTopDownSet-class
colData<-	AbstractTopDownSet-class
colData<-,AbstractTopDownSet-method	AbstractTopDownSet-class
combine	AbstractTopDownSet-class
combine,AbstractTopDownSet,AbstractTopDownSet-method	AbstractTopDownSet-class
combine,FragmentViews,FragmentViews-method	FragmentViews-class
combine,FragmentViews-method	FragmentViews-class
combine,TopDownSet,TopDownSet-method	TopDownSet-class
conditionData	AbstractTopDownSet-class
conditionData,AbstractTopDownSet-method	AbstractTopDownSet-class
conditionData<-	AbstractTopDownSet-class
conditionData<-,AbstractTopDownSet-method	AbstractTopDownSet-class
conditionNames	AbstractTopDownSet-class
conditionNames,AbstractTopDownSet-method	AbstractTopDownSet-class
createExperimentsFragmentOptimisation	createExperimentsFragmentOptimisation
createTngFusionMethFiles	windows-specific-functions
defaultMs1Settings	default-functions
defaultMs2Settings	default-functions
dim,AbstractTopDownSet-method	AbstractTopDownSet-class
dimnames,AbstractTopDownSet-method	AbstractTopDownSet-class
expandMs1Conditions	expandMsConditions
expandTms2Conditions	expandMsConditions
filterCv	TopDownSet-class
filterCv,TopDownSet-method	TopDownSet-class
filterInjectionTime	TopDownSet-class
filterInjectionTime,TopDownSet-method	TopDownSet-class
filterIntensity	TopDownSet-class
filterIntensity,TopDownSet-method	TopDownSet-class
filterNonReplicatedFragments	TopDownSet-class
filterNonReplicatedFragments,TopDownSet-method	TopDownSet-class
fragmentationMap	NCBSet-class
fragmentationMap,NCBSet-method	NCBSet-class
FragmentViews	FragmentViews-class
FragmentViews-class	FragmentViews-class
mz,FragmentViews-method	FragmentViews-class
NCBSet-class	NCBSet-class
normalize,TopDownSet-method	TopDownSet-class
plot,TopDownSet,missing-method	TopDownSet-class
readTopDownFiles	readTopDownFiles
removeEmptyConditions	AbstractTopDownSet-class
removeEmptyConditions,AbstractTopDownSet-method	AbstractTopDownSet-class
rowViews	AbstractTopDownSet-class
rowViews,AbstractTopDownSet-method	AbstractTopDownSet-class
runScanHeadsman	windows-specific-functions
runXmlMethodChanger	windows-specific-functions
show,AbstractTopDownSet-method	AbstractTopDownSet-class
show,FragmentViews-method	FragmentViews-class
show,NCBSet-method	NCBSet-class
show,TopDownSet-method	TopDownSet-class
summary,AbstractTopDownSet-method	AbstractTopDownSet-class
summary,NCBSet-method	NCBSet-class
summary,TopDownSet-method	TopDownSet-class
tds	tds
topdownr	topdownr-package
topdownr-deprecated	topdownr-deprecated
TopDownSet-class	TopDownSet-class
updateConditionNames	AbstractTopDownSet-class
updateConditionNames,AbstractTopDownSet-method	AbstractTopDownSet-class
updateMedianInjectionTime	AbstractTopDownSet-class
updateMedianInjectionTime,AbstractTopDownSet-method	AbstractTopDownSet-class
updateMedianInjectionTime,TopDownSet-method	AbstractTopDownSet-class
validMs1Settings	validMsSettings
validTms2Settings	validMsSettings
writeMethodXmls	writeMethodXmls
[,AbstractTopDownSet,ANY,ANY,ANY-method	AbstractTopDownSet-class
[[,AbstractTopDownSet,ANY,missing,-method	AbstractTopDownSet-class
[[,AbstractTopDownSet,ANY,missing-method	AbstractTopDownSet-class
[[<-,AbstractTopDownSet,ANY,missing,-method	AbstractTopDownSet-class
[[<-,AbstractTopDownSet,ANY,missing-method	AbstractTopDownSet-class
