API for sgibb/topdownr
Investigation of Fragmentation Conditions in Top-Down Proteomics
| Global functions | |
|---|---|
| $,AbstractTopDownSet-method | Man page |
| $<-,AbstractTopDownSet-method | Man page |
| AbstractTopDownSet-class | Man page |
| DollarNames.AbstractTopDownSet | Source code |
| 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 |
| addAdducts | Source code |
| aggregate,TopDownSet-method | Man page |
| aggregateDataFrame | Source code |
| all.equal.AbstractTopDownSet | Source code |
| allIdentical | Source code |
| assayData,AbstractTopDownSet-method | Man page |
| atdsLogMsg | Source code |
| bestConditions | Man page |
| bestConditions,NCBSet-method | Man page |
| bestNcbCoverageCombination | Source code |
| calculateFragments | Source code |
| calculateProteinMass | Source code |
| camelCase | Source code |
| cat0 | Source code |
| cbind | Source code |
| characterToLogical | Source code |
| coerce,FragmentViews,data.frame-method | Man page |
| coerce,TopDownSet,MSnSet-method | Man page |
| coerce,TopDownSet,NCBSet-method | Man page |
| col | Source code |
| colCounts | Source code |
| colData | Man page |
| colData,AbstractTopDownSet-method | Man page |
| colData<- | Man page |
| colData<-,AbstractTopDownSet-method | Man page |
| colSumsGroup | Source code |
| colsToLogical | Source code |
| colsToRle | Source code |
| 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 |
| condition2data.frame | Source code |
| conditionData | Man page |
| conditionData,AbstractTopDownSet-method | Man page |
| conditionData<- | Man page |
| conditionData<-,AbstractTopDownSet-method | Man page |
| conditionNames | Man page |
| conditionNames,AbstractTopDownSet-method | Man page |
| countFragments | Source code |
| createMaskMatrix | Source code |
| createTngFusionMethFiles | Man page Source code |
| cumComb | Source code |
| defaultMs1Settings | Man page Source code |
| defaultMs2Settings | Man page Source code |
| defaultSettings | Source code |
| dgcMatrix2data.frame | Source code |
| dim,AbstractTopDownSet-method | Man page |
| dimnames,AbstractTopDownSet-method | Man page |
| drop0rowLe | Source code |
| drop0rowLt | Source code |
| drop0rowReplicates | Source code |
| dropNA | Source code |
| dropNonInformativeColumns | Source code |
| droplevels | Source code |
| fileExt | 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 |
| filterStringToId | Source code |
| fixFilterString | Source code |
| fixFilterStringId | Source code |
| formatNumbers | Source code |
| fragmentType | Source code |
| fragmentationMap | Man page |
| fragmentationMap,NCBSet-method | Man page |
| fragmentationMethod | Source code |
| groupBy | Source code |
| groupByLabels | Source code |
| groupId | Source code |
| hft | Source code |
| highestNcbBondCoverage | Source code |
| highestNcbFragmentCoverage | Source code |
| listTopDownFiles | Source code |
| logdim | Source code |
| logmsg | Source code |
| makeNames | Source code |
| makeRowNames | Source code |
| massLabel | Source code |
| massLabelToId | Source code |
| matchFragments | Source code |
| mergeScanConditionAndHeaderInformation | Source code |
| mergeSpectraAndHeaderInformation | Source code |
| ms2Experiments | Source code |
| msg | Source code |
| mz,FragmentViews-method | Man page |
| ncbMap | Source code |
| ndigits | Source code |
| nheritsAbstractTopDownSet | Source code |
| normaliseCols | Source code |
| normaliseRows | Source code |
| normalize,TopDownSet-method | Man page |
| nrows | Source code |
| onAttach | Source code |
| orderByColumns | Source code |
| plot | Source code |
| plot,TopDownSet,missing-method | Man page |
| rbind | Source code |
| readExperimentCsv | Source code |
| readFasta | Source code |
| readMzMl | Source code |
| readScanHeadsTable | Source code |
| readSpectrum | Source code |
| readTopDownFiles | Man page Source code |
| removeEmptyConditions | Man page |
| removeEmptyConditions,AbstractTopDownSet-method | Man page |
| removeNcbCombinations | Source code |
| reorderSequence | Source code |
| replaceZeroETDReactionTime | 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 |
| rowViews | Man page |
| rowViews,AbstractTopDownSet-method | Man page |
| runScanHeadsman | Man page Source code |
| runXmlMethodChanger | Man page |
| sCharacterCol | Source code |
| sEqual | Source code |
| sNumCol | Source code |
| sTopDownSet | Source code |
| scanHeadsman | Source code |
| show,AbstractTopDownSet-method | Man page |
| show,FragmentViews-method | Man page |
| show,NCBSet-method | Man page |
| show,TopDownSet-method | Man page |
| snippet | Source code |
| startEndTime | Source code |
| subset | Source code |
| subsetByCharacter | Source code |
| subsetByLogical | Source code |
| subsetByNumeric | Source code |
| subsetFiles | Source code |
| summary | Source code |
| summary,AbstractTopDownSet-method | Man page |
| summary,NCBSet-method | Man page |
| summary,TopDownSet-method | Man page |
| swapFileExt | Source code |
| targetedMassListToMz | Source code |
| tds | Man page |
| topDownFileExtRx | Source code |
| topIdx | Source code |
| topdownr | Man page |
| topdownr-package | Man page |
| translateThermoIdToScanId | Source code |
| unimod1 | Source code |
| unimod4 | Source code |
| unimod765 | Source code |
| updateConditionNames | Man page |
| updateConditionNames,AbstractTopDownSet-method | Man page |
| updateMedianInjectionTime | Man page |
| updateMedianInjectionTime,AbstractTopDownSet-method | Man page |
| updateMedianInjectionTime,TopDownSet-method | Man page |
| validMs1Tags | Source code |
| validMs2Tags | Source code |
| validateAbstractTopDownSet | Source code |
| validateFragmentViews | Source code |
| validateNCBSet | Source code |
| vapply1d | Source code |
| vapply1l | Source code |
| writeMethodXml | Source code |
| writeMethodXmls | Man page Source code |
| xmlCopyAndAppendExperiment | Source code |
| xmlFullMsScan | Source code |
| xmlHeader | Source code |
| xmlListToTags | Source code |
| xmlMassList | Source code |
| xmlMassListRecord | Source code |
| xmlMethodChanger | Source code |
| xmlStartEndTime | Source code |
| xmlTMSnScan | Source code |
| xmlTag | Source code |
| xmlTagClose | Source code |
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