Investigation of Fragmentation Conditions in Top-Down Proteomics

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Documentation for package ‘topdownr’ version 1.27.0

• 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.
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