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

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Man pages
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AbstractTopDownSet-class: The AbstractTopDownSet class default-functions: Settings for MS1/2 parameters. FragmentViews-class: The FragmentViews class readTopDownFiles: Read top-down files. topdownr-package: Investigation of Fragmentation Conditions in Top-Down... windows-specific-functions: Windows specific functions. writeMethodXmls: Create Orbitrap Fusion method.xml files.
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API
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writeMethodXmls runScanHeadsman runXmlMethodChanger createTngFusionMethFiles topdownr-package topdownr tds
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Source code
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tests/testthat/test_utils.R tests/testthat/test_method-xml.R tests/testthat/test_import.R tests/testthat/test_fragments.R tests/testthat/test_default-functions.R tests/testthat/test_data.frame.R tests/testthat/test_coverage.R
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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
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
sgibb/topdownr documentation built on Feb. 25, 2018, 3:47 p.m.

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