sgibb/topdownr
Investigation of Fragmentation Conditions in Top-Down Proteomics

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Search the sgibb/topdownr package
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Functions
214
Source code
39
Man pages
13
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sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics
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API

API for sgibb/topdownr
Investigation of Fragmentation Conditions in Top-Down Proteomics

Global functions
$,AbstractTopDownSet-method Man page
$<-,AbstractTopDownSet-method Man page
.DollarNames.AbstractTopDownSet Source code
.addAdducts Source code
.addCustomModifications 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
.cusmod 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
sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.

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