API for Roestlab/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 |
| 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 |
| alignTargetedRuns2 | Man page Source code |
| alignToMaster | Man page Source code |
| alignToRef | Man page Source code |
| alignedTimes2 | Source code |
| alignedXIC | Man page Source code |
| alignmentStats | Man page Source code |
| analytesFromFeatures | Man page 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 | Source code |
| childXICs | Man page Source code |
| chromatogramIdAsInteger | Man page Source code |
| constrainSimCpp | Source code |
| createMZML | Man page Source code |
| createSqMass | Man page Source code |
| dialignrLoess | Man page 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 |
| 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 |
| getChildFeature | Man page Source code |
| getChildXICpp | Man page Source code |
| getChildXICs | 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 |
| getMZMLpointers | Man page |
| getMappedRT | Man page Source code |
| getMultipeptide | Man page Source code |
| getNodeIDs | Man page Source code |
| getNodeRun | Man page Source code |
| getOswAnalytes | Man page Source code |
| getOswFiles | Source code |
| getPeptideQuery | Man page Source code |
| getPeptideQuery2 | Man page Source code |
| getPeptideScores | Man page |
| getPrecursorByID | Man page |
| 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 |
| 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 |
| getXICs | Man page Source code |
| getXICs4AlignObj | Man page Source code |
| get_ropenms | Man page Source code |
| imputeChromatogram | 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 |
| multipeptide_DIAlignR | Man page |
| newRow | Source code |
| notReady | Source code |
| nrDesc | Man page Source code |
| oswFiles_DIAlignR | Man page |
| otherChildXICpp | Man page Source code |
| parFUN1 | Source code |
| paramsDIAlignR | Man page Source code |
| perBatch | Source code |
| pickNearestFeature | Man page Source code |
| plotAlignedAnalytes | Man page |
| plotAlignmentPath | Man page |
| plotAnalyteXICs | Man page |
| plotSingleAlignedChrom | Man page |
| plotXICgroup | Man page |
| progAlignRuns | Man page Source code |
| progAlignRuns2 | Man page Source code |
| reIntensity | Source code |
| reIntensity2 | Source code |
| readMzMLHeader | Man page |
| readSqMassHeader | Man page |
| recalculateIntensity | Man page Source code |
| script1 | Man page |
| setAlignmentRank | Man page Source code |
| setOtherPrecursors | 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 | Source code |
| splineFillCpp | Man page Source code |
| testAlignObj | Source code |
| traverseDown | 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 |
| writeTables | Man page Source code |
| xicIntersect | Source code |
