Reference

All functions

`[`(<AbstractTopDownSet>,<ANY>,<ANY>,<ANY>) `[[`(<AbstractTopDownSet>,<ANY>,<missing>) `[[<-`(<AbstractTopDownSet>,<ANY>,<missing>) `$`(<AbstractTopDownSet>) `$<-`(<AbstractTopDownSet>) assayData(<AbstractTopDownSet>) colData(<AbstractTopDownSet>) `colData<-`(<AbstractTopDownSet>) combine(<AbstractTopDownSet>,<AbstractTopDownSet>) conditionData(<AbstractTopDownSet>) `conditionData<-`(<AbstractTopDownSet>) conditionNames(<AbstractTopDownSet>) dim(<AbstractTopDownSet>) dimnames(<AbstractTopDownSet>) removeEmptyConditions(<AbstractTopDownSet>) rowViews(<AbstractTopDownSet>) show(<AbstractTopDownSet>) summary(<AbstractTopDownSet>) updateConditionNames(<AbstractTopDownSet>) updateMedianInjectionTime(<AbstractTopDownSet>)

The AbstractTopDownSet class

FragmentViews() combine(<FragmentViews>,<FragmentViews>) mz(<FragmentViews>) show(<FragmentViews>)

The FragmentViews class

bestConditions(<NCBSet>) fragmentationMap(<NCBSet>) show(<NCBSet>) summary(<NCBSet>)

The NCBSet class

aggregate(<TopDownSet>) combine(<TopDownSet>,<TopDownSet>) filterCv(<TopDownSet>) filterInjectionTime(<TopDownSet>) filterIntensity(<TopDownSet>) filterNonReplicatedFragments(<TopDownSet>) normalize(<TopDownSet>) plot(<TopDownSet>,<missing>) show(<TopDownSet>) summary(<TopDownSet>)

The TopDownSet class

createExperimentsFragmentOptimisation()

Create fragment optimisation experiment

expandMs1Conditions() expandTms2Conditions()

Expand MS Conditions

readTopDownFiles()

Read top-down files.

tds

TopDownSet Example Data

topdownr-deprecated

Deprecated functions in topdownr

topdownr-package

Investigation of Fragmentation Conditions in Top-Down Proteomics

validMs1Settings() validTms2Settings()

List valid MS settings.

createTngFusionMethFiles() runXmlMethodChanger() runScanHeadsman()

Windows specific functions.

writeMethodXmls()

Create Orbitrap Fusion Lumos method.xml files.