API for shubham1637/DIAlign
Dynamic Programming Based Alignment of MS2 Chromatograms

Global functions
AffineAlignObj Man page
AffineAlignObj-class Man page
AffineAlignObjLight Man page
AffineAlignObjLight-class Man page
AffineAlignObjMedium Man page
AffineAlignObjMedium-class Man page
AlignObj Man page
AlignObj-class Man page
DIAlignR Man page
MSTperBatch Man page Source code
XIC_QFNNTDIVLLEDFQK_3_DIAlignR Man page
addFlankToLeft Man page Source code
addFlankToRight Man page Source code
addMasterToOSW Source code
addXIC Man page Source code
akimaFill Source code
alignChromatogramsCpp Man page Source code
alignObj_DIAlignR Man page
alignTargetedRuns Man page Source code
alignToMaster Man page Source code
alignToRef Man page Source code
alignToRefMST Man page Source code
alignToRoot Source code
alignToRoot4 Man page Source code
alignedTimes2 Source code
alignedXIC Man page Source code
alignmentStats Man page Source code
analytesFromFeatures Man page Source code
ancesTree Source code
approxFill Man page Source code
areaIntegrator Man page Source code
as.list,AffineAlignObj-method Man page
as.list,AffineAlignObjLight-method Man page
as.list,AffineAlignObjMedium-method Man page
as.list,AlignObj-method Man page
blobXICs Man page Source code
calculateIntensity Man page Source code
checkOverlap Man page Source code
checkParams Man page Source code
childXIC Man page Source code
childXICs Man page Source code
chromatogramIdAsInteger Man page Source code
constrainSimCpp Man page Source code
createMZML Man page Source code
createSqMass Man page Source code
createTemp Source code
cutTree Source code
dialignrLoess Man page Source code
dist4split Source code
doAffineAlignmentCpp Man page Source code
doAlignmentCpp Man page Source code
dummyChromIndex Source code
dummyMerge Source code
dummyTbl Source code
extractXIC_group Man page Source code
extractXIC_group2 Man page Source code
fetchAnalytesInfo Man page Source code
fetchFeaturesFromRun Man page
fetchPeptidesInfo Man page
fetchPeptidesInfo2 Man page
fetchPrecursorsInfo Man page Source code
fetchTransitionsFromRun Man page
filenamesFromMZML Man page Source code
filenamesFromOSW Man page Source code
getAlignObj Man page Source code
getAlignObj2 Source code
getAlignObjs Man page Source code
getAlignedFigs Man page Source code
getAlignedIndices Man page Source code
getAlignedTimes Man page Source code
getAlignedTimesCpp Man page Source code
getAlignedTimesFast Man page Source code
getAnalytesQuery Man page Source code
getBaseGapPenaltyCpp Man page Source code
getBestPkIdx Source code
getChildFeature Man page Source code
getChildXICpp Man page Source code
getChildXICs Man page Source code
getChromSimMatCpp Man page Source code
getChromatogramIndices Man page Source code
getFeatures Man page
getFeaturesQuery Man page Source code
getGlobalAlignMaskCpp Man page Source code
getGlobalAlignment Man page Source code
getGlobalFits Man page Source code
getLOESSfit Man page Source code
getLinearfit Man page Source code
getMST Man page Source code
getMZMLpointers Man page Source code
getMappedRT Man page Source code
getMultipeptide Man page Source code
getNativeIDs Man page Source code
getNodeIDs Man page Source code
getNodeRun Man page Source code
getOswAnalytes Man page Source code
getOswFiles Man page Source code
getPeptideQuery Man page Source code
getPeptideQuery2 Man page Source code
getPeptideScores Man page
getPrecursorByID Man page
getPrecursorIndices Man page Source code
getPrecursorSubset Man page Source code
getPrecursors Man page
getPrecursorsQuery Man page Source code
getPrecursorsQueryID Man page Source code
getQuery Man page Source code
getRSE Man page Source code
getRTdf Man page Source code
getRefExpFeatureMap Man page Source code
getRefRun Man page Source code
getRunNames Man page Source code
getSeqSimMatCpp Man page Source code
getTransitions Man page
getTransitionsQuery Man page Source code
getTree Man page Source code
getUpperTree Source code
getXICs Man page Source code
getXICs4AlignObj Man page Source code
get_ropenms Man page Source code
imputeChromatogram Man page Source code
ipfReassignFDR Man page Source code
mapIdxToTime Man page Source code
mapPrecursorToChromIndices Man page Source code
mappedRTfromAlignObj Man page Source code
masterXICs_DIAlignR Man page
mergeOswAnalytes_ChromHeader Man page Source code
mergeXIC Man page Source code
mstAlignRuns Man page Source code
mstScript1 Man page Source code
mstScript2 Man page Source code
multipeptide_DIAlignR Man page
newRow Source code
notReady Source code
nrDesc Man page Source code
oswFiles_DIAlignR Man page
otherChildXICpp Man page Source code
overlapLen Source code
parFUN1 Source code
paramsDIAlignR Man page Source code
perBatch Man page Source code
pickNearestFeature Man page Source code
pkDist Source code
plotAlignedAnalytes Man page Source code
plotAlignmentPath Man page Source code
plotAnalyteXICs Man page Source code
plotSingleAlignedChrom Man page Source code
plotXICgroup Man page Source code
populateReferenceExperimentFeatureAlignmentMap Man page Source code
progAlignRuns Man page Source code
progComb3 Man page Source code
progSplit2 Man page Source code
progSplit4 Man page Source code
progTree1 Man page Source code
reIntensity Source code
reIntensity2 Source code
readMzMLHeader Man page Source code
readSqMassHeader Man page Source code
recalculateIntensity Man page Source code
reduceXICs Man page Source code
script1 Man page Source code
script2 Man page Source code
setAlignmentRank Man page Source code
setOtherPrecursors Source code
setRootRank Source code
sgolayCpp Man page Source code
sgolayFill Man page Source code
skip_if_no_pyopenms Source code
smoothSingleXIC Man page Source code
smoothXICs Man page Source code
splineFill Man page Source code
splineFillCpp Man page Source code
sqMassQuery Source code
testAlignObj Source code
testtAligned Source code
totalIntensity Source code
traverseDown Man page Source code
traverseMST Man page Source code
traverseUp Man page Source code
trfrParentFeature Man page Source code
trimXICs Man page Source code
uncompressVec Man page Source code
updateFileInfo Man page Source code
updateOnalignTargetedRuns Man page Source code
writeOutFeatureAlignmentMap Man page Source code
writeTables Man page Source code
xicIntersect Source code
shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.