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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