Global functions | |
---|---|
$,AbstractTopDownSet-method | Man page |
$<-,AbstractTopDownSet-method | Man page |
.DollarNames.AbstractTopDownSet | Source code |
.addAdducts | Source code |
.aggregateDataFrame | Source code |
.allIdentical | Source code |
.atdsLogMsg | Source code |
.bestNcbCoverageCombination | Source code |
.calculateFragments | Source code |
.calculateProteinMass | Source code |
.camelCase | Source code |
.cbind | Source code |
.characterToLogical | Source code |
.col | Source code |
.colCounts | Source code |
.colSumsGroup | Source code |
.collapseMassList | Source code |
.colsToLogical | Source code |
.colsToRle | Source code |
.condition2data.frame | Source code |
.copyAndAppendExperiment | Source code |
.countFragments | Source code |
.createMaskMatrix | Source code |
.cumComb | Source code |
.dgcMatrix2data.frame | Source code |
.drop0rowLe | Source code |
.drop0rowLt | Source code |
.drop0rowReplicates | Source code |
.dropNA | Source code |
.dropNaColumns | Source code |
.dropNonInformativeColumns | Source code |
.droplevels | Source code |
.expandMassList | Source code |
.fileExt | Source code |
.filterStringToId | Source code |
.fixFilterString | Source code |
.fixFilterStringId | Source code |
.flatten | Source code |
.formatNumbers | Source code |
.fragmentationMethod | Source code |
.groupBy | Source code |
.groupByLabels | Source code |
.groupId | Source code |
.hft | Source code |
.highestNcbBondCoverage | Source code |
.highestNcbFragmentCoverage | Source code |
.inheritsAbstractTopDownSet | Source code |
.isCharacterCol | Source code |
.isEqual | Source code |
.isNumCol | Source code |
.isTopDownSet | Source code |
.listTopDownFiles | Source code |
.logdim | Source code |
.logmsg | Source code |
.makeNames | Source code |
.makeRowNames | Source code |
.massLabel | Source code |
.massLabelToId | Source code |
.massListToTree | Source code |
.matchFragments | Source code |
.mergeScanConditionAndHeaderInformation | Source code |
.mergeSpectraAndHeaderInformation | Source code |
.ms1ConditionToTree | Source code |
.msg | Source code |
.ncbMap | Source code |
.ndigits | Source code |
.normaliseCols | Source code |
.normaliseRows | Source code |
.nrows | Source code |
.onAttach | Source code |
.orderByColumns | Source code |
.plot | Source code |
.rbind | Source code |
.readExperimentCsv | Source code |
.readFasta | Source code |
.readMzMl | Source code |
.readScanHeadsTable | Source code |
.readSpectrum | Source code |
.removeNcbCombinations | Source code |
.reorderSequence | Source code |
.resample | Source code |
.row | Source code |
.rowCounts | Source code |
.rowCvsGroup | Source code |
.rowMax | Source code |
.rowMeansGroup | Source code |
.rowSdsGroup | Source code |
.rowSumsGroup | Source code |
.rtToScanId | Source code |
.scanDescription | Source code |
.scanHeadsman | Source code |
.snippet | Source code |
.startEndTime | Source code |
.subset | Source code |
.subsetByCharacter | Source code |
.subsetByLogical | Source code |
.subsetByNumeric | Source code |
.subsetFiles | Source code |
.summary | Source code |
.swapFileExt | Source code |
.targetedMassListToMz | Source code |
.tms2ConditionToTree | Source code |
.topDownFileExtRx | Source code |
.topIdx | Source code |
.translateThermoIdToScanId | Source code |
.unimod1 | Source code |
.unimod4 | Source code |
.unimod765 | Source code |
.validFilename | Source code |
.validMsSettings | Source code |
.validateAbstractTopDownSet | Source code |
.validateFragmentViews | Source code |
.validateMsSetting | Source code |
.validateMsSettings | Source code |
.validateNCBSet | Source code |
.vapply1d | Source code |
.vapply1l | Source code |
.xmlChildrenNameType | Source code |
.xmlEnumeration | Source code |
.xmlMethodChanger | Source code |
.xmlTmsnScanParameters | Source code |
.xmlValidMsSettings | Source code |
AbstractTopDownSet-class | Man page |
FragmentViews | Man page Source code |
FragmentViews-class | Man page |
NCBSet-class | Man page |
TopDownSet-class | Man page |
[,AbstractTopDownSet,ANY,ANY,ANY-method | Man page |
[[,AbstractTopDownSet,ANY,missing,-method | Man page |
[[,AbstractTopDownSet,ANY,missing-method | Man page |
[[<-,AbstractTopDownSet,ANY,missing,-method | Man page |
[[<-,AbstractTopDownSet,ANY,missing-method | Man page |
aggregate,TopDownSet-method | Man page |
all.equal.AbstractTopDownSet | Source code |
assayData,AbstractTopDownSet-method | Man page |
bestConditions | Man page |
bestConditions,NCBSet-method | Man page |
cat0 | Source code |
coerce,FragmentViews,data.frame-method | Man page |
coerce,TopDownSet,MSnSet-method | Man page |
coerce,TopDownSet,NCBSet-method | Man page |
colData | Man page |
colData,AbstractTopDownSet-method | Man page |
colData<- | Man page |
colData<-,AbstractTopDownSet-method | Man page |
combine | Man page |
combine,AbstractTopDownSet,AbstractTopDownSet-method | Man page |
combine,FragmentViews,FragmentViews-method | Man page |
combine,FragmentViews-method | Man page |
combine,TopDownSet,TopDownSet-method | Man page |
conditionData | Man page |
conditionData,AbstractTopDownSet-method | Man page |
conditionData<- | Man page |
conditionData<-,AbstractTopDownSet-method | Man page |
conditionNames | Man page |
conditionNames,AbstractTopDownSet-method | Man page |
createExperimentsFragmentOptimisation | Man page Source code |
createTngFusionMethFiles | Man page Source code |
dim,AbstractTopDownSet-method | Man page |
dimnames,AbstractTopDownSet-method | Man page |
expandMs1Conditions | Man page Source code |
expandTms2Conditions | Man page Source code |
filterCv | Man page |
filterCv,TopDownSet-method | Man page |
filterInjectionTime | Man page |
filterInjectionTime,TopDownSet-method | Man page |
filterIntensity | Man page |
filterIntensity,TopDownSet-method | Man page |
filterNonReplicatedFragments | Man page |
filterNonReplicatedFragments,TopDownSet-method | Man page |
fragmentType | Source code |
fragmentationMap | Man page |
fragmentationMap,NCBSet-method | Man page |
mz,FragmentViews-method | Man page |
normalize,TopDownSet-method | Man page |
plot,TopDownSet,missing-method | Man page |
readTopDownFiles | Man page Source code |
removeEmptyConditions | Man page |
removeEmptyConditions,AbstractTopDownSet-method | Man page |
rowViews | Man page |
rowViews,AbstractTopDownSet-method | Man page |
runScanHeadsman | Man page Source code |
runXmlMethodChanger | Man page |
show,AbstractTopDownSet-method | Man page |
show,FragmentViews-method | Man page |
show,NCBSet-method | Man page |
show,TopDownSet-method | Man page |
summary,AbstractTopDownSet-method | Man page |
summary,NCBSet-method | Man page |
summary,TopDownSet-method | Man page |
tds | Man page |
topdownr | Man page |
topdownr-deprecated | Man page |
topdownr-package | Man page |
updateConditionNames | Man page |
updateConditionNames,AbstractTopDownSet-method | Man page |
updateMedianInjectionTime | Man page |
updateMedianInjectionTime,AbstractTopDownSet-method | Man page |
updateMedianInjectionTime,TopDownSet-method | Man page |
validMs1Settings | Man page Source code |
validTms2Settings | Man page Source code |
writeMethodXmls | Man page Source code |
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