# Investigation of Fragmentation Conditions in Top-Down Proteomics

## Documentation for package ‘topdownr’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

topdownr-package | Investigation of Fragmentation Conditions in Top-Down Proteomics
$-method | The AbstractTopDownSet class
$<--method | The AbstractTopDownSet class
AbstractTopDownSet-class | The AbstractTopDownSet class
aggregate-method | The TopDownSet class
assayData-method | The AbstractTopDownSet class
bestConditions | The NCBSet class
bestConditions-method | The NCBSet class
coerce-method | The FragmentViews class
coerce-method | The TopDownSet class
colData | The AbstractTopDownSet class
colData-method | The AbstractTopDownSet class
colData<- | The AbstractTopDownSet class
colData<--method | The AbstractTopDownSet class
combine | The AbstractTopDownSet class
combine-method | The AbstractTopDownSet class
combine-method | The FragmentViews class
combine-method | The TopDownSet class
conditionData | The AbstractTopDownSet class
conditionData-method | The AbstractTopDownSet class
conditionData<- | The AbstractTopDownSet class
conditionData<--method | The AbstractTopDownSet class
conditionNames | The AbstractTopDownSet class
conditionNames-method | The AbstractTopDownSet class
createExperimentsFragmentOptimisation | Create fragment optimisation experiment
createTngFusionMethFiles | Windows specific functions.
defaultMs1Settings | Settings for MS1/2 parameters.
defaultMs2Settings | Settings for MS1/2 parameters.
dim-method | The AbstractTopDownSet class
dimnames-method | The AbstractTopDownSet class
expandMs1Conditions | Expand MS Conditions
expandTms2Conditions | Expand MS Conditions
filterCv | The TopDownSet class
filterCv-method | The TopDownSet class
filterInjectionTime | The TopDownSet class
filterInjectionTime-method | The TopDownSet class
filterIntensity | The TopDownSet class
filterIntensity-method | The TopDownSet class
filterNonReplicatedFragments | The TopDownSet class
filterNonReplicatedFragments-method | The TopDownSet class
fragmentationMap | The NCBSet class
fragmentationMap-method | The NCBSet class
FragmentViews | The FragmentViews class
FragmentViews-class | The FragmentViews class
mz-method | The FragmentViews class
NCBSet-class | The NCBSet class
normalize-method | The TopDownSet class
plot-method | The TopDownSet class
readTopDownFiles | Read top-down files.
removeEmptyConditions | The AbstractTopDownSet class
removeEmptyConditions-method | The AbstractTopDownSet class
rowViews | The AbstractTopDownSet class
rowViews-method | The AbstractTopDownSet class
runScanHeadsman | Windows specific functions.
runXmlMethodChanger | Windows specific functions.
show-method | The AbstractTopDownSet class
show-method | The FragmentViews class
show-method | The NCBSet class
show-method | The TopDownSet class
summary-method | The AbstractTopDownSet class
summary-method | The NCBSet class
summary-method | The TopDownSet class
tds | TopDownSet Example Data
topdownr | Investigation of Fragmentation Conditions in Top-Down Proteomics
topdownr-deprecated | Deprecated functions in topdownr
TopDownSet-class | The TopDownSet class
updateConditionNames | The AbstractTopDownSet class
updateConditionNames-method | The AbstractTopDownSet class
updateMedianInjectionTime | The AbstractTopDownSet class
updateMedianInjectionTime-method | The AbstractTopDownSet class
validMs1Settings | List valid MS settings.
validTms2Settings | List valid MS settings.
writeMethodXmls | Create Orbitrap Fusion Lumos method.xml files.
[-method | The AbstractTopDownSet class
[[-method | The AbstractTopDownSet class
[[<--method | The AbstractTopDownSet class