addFlankToLeft	addFlankToLeft
addFlankToRight	addFlankToRight
addXIC	addXIC
AffineAlignObj	AffineAlignObj-class
AffineAlignObj-class	AffineAlignObj-class
AffineAlignObjLight	AffineAlignObjLight-class
AffineAlignObjLight-class	AffineAlignObjLight-class
AffineAlignObjMedium	AffineAlignObjMedium-class
AffineAlignObjMedium-class	AffineAlignObjMedium-class
alignChromatogramsCpp	alignChromatogramsCpp
alignedXIC	alignedXIC
alignmentStats	alignmentStats
AlignObj	AlignObj-class
AlignObj-class	AlignObj-class
alignObj_DIAlignR	alignObj_DIAlignR
alignTargetedRuns	alignTargetedRuns
alignToMaster	alignToMaster
alignToRef	alignToRef
alignToRefMST	alignToRefMST
alignToRoot4	alignToRoot4
analytesFromFeatures	analytesFromFeatures
approxFill	approxFill
areaIntegrator	areaIntegrator
as.list,AffineAlignObj-method	as.list-AffineAlignObj-method
as.list,AffineAlignObjLight-method	as.list-AffineAlignObjLight-method
as.list,AffineAlignObjMedium-method	as.list-AffineAlignObjMedium-method
as.list,AlignObj-method	as.list-AlignObj-method
blobXICs	blobXICs
calculateIntensity	calculateIntensity
checkOverlap	checkOverlap
checkParams	checkParams
childXIC	childXIC
childXICs	childXICs
chromatogramIdAsInteger	chromatogramIdAsInteger
constrainSimCpp	constrainSimCpp
createMZML	createMZML
createSqMass	createSqMass
DIAlignR	DIAlignR
dialignrLoess	dialignrLoess
doAffineAlignmentCpp	doAffineAlignmentCpp
doAlignmentCpp	doAlignmentCpp
extractXIC_group	extractXIC_group
extractXIC_group2	extractXIC_group2
fetchAnalytesInfo	fetchAnalytesInfo
fetchFeaturesFromRun	fetchFeaturesFromRun
fetchPeptidesInfo	fetchPeptidesInfo
fetchPeptidesInfo2	fetchPeptidesInfo2
fetchPrecursorsInfo	fetchPrecursorsInfo
fetchTransitionsFromRun	fetchTransitionsFromRun
filenamesFromMZML	filenamesFromMZML
filenamesFromOSW	filenamesFromOSW
getAlignedFigs	getAlignedFigs
getAlignedIndices	getAlignedIndices
getAlignedTimes	getAlignedTimes
getAlignedTimesCpp	getAlignedTimesCpp
getAlignedTimesFast	getAlignedTimesFast
getAlignObj	getAlignObj
getAlignObjs	getAlignObjs
getAnalytesQuery	getAnalytesQuery
getBaseGapPenaltyCpp	getBaseGapPenaltyCpp
getChildFeature	getChildFeature
getChildXICpp	getChildXICpp
getChildXICs	getChildXICs
getChromatogramIndices	getChromatogramIndices
getChromSimMatCpp	getChromSimMatCpp
getFeatures	getFeatures
getFeaturesQuery	getFeaturesQuery
getGlobalAlignMaskCpp	getGlobalAlignMaskCpp
getGlobalAlignment	getGlobalAlignment
getGlobalFits	getGlobalFits
getLinearfit	getLinearfit
getLOESSfit	getLOESSfit
getMappedRT	getMappedRT
getMST	getMST
getMultipeptide	getMultipeptide
getMZMLpointers	getMZMLpointers
getNativeIDs	getNativeIDs
getNodeIDs	getNodeIDs
getNodeRun	getNodeRun
getOswAnalytes	getOswAnalytes
getOswFiles	getOswFiles
getPeptideQuery	getPeptideQuery
getPeptideQuery2	getPeptideQuery2
getPeptideScores	getPeptideScores
getPrecursorByID	getPrecursorByID
getPrecursorIndices	getPrecursorIndices
getPrecursors	getPrecursors
getPrecursorsQuery	getPrecursorsQuery
getPrecursorsQueryID	getPrecursorsQueryID
getPrecursorSubset	getPrecursorSubset
getQuery	getQuery
getRefExpFeatureMap	getRefExpFeatureMap
getRefRun	getRefRun
getRSE	getRSE
getRTdf	getRTdf
getRunNames	getRunNames
getSeqSimMatCpp	getSeqSimMatCpp
getTransitions	getTransitions
getTransitionsQuery	getTransitionsQuery
getTree	getTree
getXICs	getXICs
getXICs4AlignObj	getXICs4AlignObj
get_ropenms	get_ropenms
imputeChromatogram	imputeChromatogram
ipfReassignFDR	ipfReassignFDR
mapIdxToTime	mapIdxToTime
mappedRTfromAlignObj	mappedRTfromAlignObj
mapPrecursorToChromIndices	mapPrecursorToChromIndices
masterXICs_DIAlignR	masterXICs_DIAlignR
mergeOswAnalytes_ChromHeader	mergeOswAnalytes_ChromHeader
mergeXIC	mergeXIC
mstAlignRuns	mstAlignRuns
MSTperBatch	MSTperBatch
mstScript1	mstScript1
mstScript2	mstScript2
multipeptide_DIAlignR	multipeptide_DIAlignR
nrDesc	nrDesc
oswFiles_DIAlignR	oswFiles_DIAlignR
otherChildXICpp	otherChildXICpp
paramsDIAlignR	paramsDIAlignR
perBatch	perBatch
pickNearestFeature	pickNearestFeature
plotAlignedAnalytes	plotAlignedAnalytes
plotAlignmentPath	plotAlignmentPath
plotAnalyteXICs	plotAnalyteXICs
plotSingleAlignedChrom	plotSingleAlignedChrom
plotXICgroup	plotXICgroup
populateReferenceExperimentFeatureAlignmentMap	populateReferenceExperimentFeatureAlignmentMap
progAlignRuns	progAlignRuns
progComb3	progComb3
progSplit2	progSplit2
progSplit4	progSplit4
progTree1	progTree1
readMzMLHeader	readMzMLHeader
readSqMassHeader	readSqMassHeader
recalculateIntensity	recalculateIntensity
reduceXICs	reduceXICs
script1	script1
script2	script2
setAlignmentRank	setAlignmentRank
sgolayCpp	sgolayCpp
sgolayFill	sgolayFill
smoothSingleXIC	smoothSingleXIC
smoothXICs	smoothXICs
splineFill	splineFill
splineFillCpp	splineFillCpp
traverseDown	traverseDown
traverseMST	traverseMST
traverseUp	traverseUp
trfrParentFeature	trfrParentFeature
trimXICs	trimXICs
uncompressVec	uncompressVec
updateFileInfo	updateFileInfo
updateOnalignTargetedRuns	updateOnalignTargetedRuns
writeOutFeatureAlignmentMap	writeOutFeatureAlignmentMap
writeTables	writeTables
XIC_QFNNTDIVLLEDFQK_3_DIAlignR	XIC_QFNNTDIVLLEDFQK_3_DIAlignR
