├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── CMakeLists.txt ├── DESCRIPTION ├── DIAlignR.Rproj ├── NAMESPACE ├── NEWS ├── R ├── DIAlignR.R ├── RcppExports.R ├── affine_aligned_obj.R ├── align_dia_runs.R ├── chromatogram_manip.R ├── data.R ├── fill_missing_intensity.R ├── get_analytes.R ├── get_filenames.R ├── get_global_fit.R ├── get_osw_query.R ├── get_peaks_chromatograms.R ├── merge_chromatogram.R ├── merge_order.R ├── merge_osw_mzml.R ├── merge_runs.R ├── nature_paper.R ├── pairwise_pep_peak_corp.R ├── peak_area.R ├── post_alignment.R ├── progressive_alignment.R ├── pyopenms.R ├── read_mzml.R ├── read_osw.R ├── scripts.R ├── sqMass.R ├── utils.R └── visualise_chromatograms.R ├── README.md ├── TODO ├── data-raw ├── test_GenerateChroms.txt └── test_GenerateData.R ├── data ├── XIC_QFNNTDIVLLEDFQK_3_DIAlignR.rda ├── alignObj_DIAlignR.rda ├── masterXICs_DIAlignR.rda ├── multipeptide_DIAlignR.rda └── oswFiles_DIAlignR.rda ├── inst ├── buildDIAlignR.txt ├── extdata │ ├── osw │ │ └── merged.osw │ └── xics │ │ ├── hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt.chrom.mzML │ │ ├── hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt.chrom.sqMass │ │ ├── hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML │ │ ├── hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt.chrom.sqMass │ │ ├── hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML │ │ └── hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.sqMass └── metabo │ ├── osw │ └── merged.osw │ └── xics │ ├── PestMix1_8Step1Plasma1SWATH20-50.chrom.mzML │ └── PestMix1_8Step8Plasma1SWATH20-50.chrom.mzML ├── man ├── AffineAlignObj-class.Rd ├── AffineAlignObjLight-class.Rd ├── AffineAlignObjMedium-class.Rd ├── AlignObj-class.Rd ├── DIAlignR.Rd ├── XIC_QFNNTDIVLLEDFQK_3_DIAlignR.Rd ├── addFlankToLeft.Rd ├── addFlankToRight.Rd ├── addXIC.Rd ├── alignChromatogramsCpp.Rd ├── alignObj_DIAlignR.Rd ├── alignTargetedRuns.Rd ├── alignTargetedRuns2.Rd ├── alignToMaster.Rd ├── alignToRef.Rd ├── alignedXIC.Rd ├── alignmentStats.Rd ├── analytesFromFeatures.Rd ├── approxFill.Rd ├── areaIntegrator.Rd ├── as.list-AffineAlignObj-method.Rd ├── as.list-AffineAlignObjLight-method.Rd ├── as.list-AffineAlignObjMedium-method.Rd ├── as.list-AlignObj-method.Rd ├── blobXICs.Rd ├── calculateIntensity.Rd ├── checkOverlap.Rd ├── checkParams.Rd ├── childXIC.Rd ├── childXICs.Rd ├── chromatogramIdAsInteger.Rd ├── constrainSimCpp.Rd ├── createMZML.Rd ├── createSqMass.Rd ├── dialignrLoess.Rd ├── doAffineAlignmentCpp.Rd ├── doAlignmentCpp.Rd ├── extractXIC_group.Rd ├── extractXIC_group2.Rd ├── fetchAnalytesInfo.Rd ├── fetchFeaturesFromRun.Rd ├── fetchPeptidesInfo.Rd ├── fetchPeptidesInfo2.Rd ├── fetchPrecursorsInfo.Rd ├── fetchTransitionsFromRun.Rd ├── filenamesFromMZML.Rd ├── filenamesFromOSW.Rd ├── getAlignObj.Rd ├── getAlignObjs.Rd ├── getAlignedFigs.Rd ├── getAlignedIndices.Rd ├── getAlignedTimes.Rd ├── getAlignedTimesCpp.Rd ├── getAlignedTimesFast.Rd ├── getAnalytesQuery.Rd ├── getBaseGapPenaltyCpp.Rd ├── getChildFeature.Rd ├── getChildXICpp.Rd ├── getChildXICs.Rd ├── getChromSimMatCpp.Rd ├── getChromatogramIndices.Rd ├── getFeatures.Rd ├── getFeaturesQuery.Rd ├── getGlobalAlignMaskCpp.Rd ├── getGlobalAlignment.Rd ├── getGlobalFits.Rd ├── getLOESSfit.Rd ├── getLinearfit.Rd ├── getMZMLpointers.Rd ├── getMappedRT.Rd ├── getMultipeptide.Rd ├── getNodeIDs.Rd ├── getNodeRun.Rd ├── getOswAnalytes.Rd ├── getOswFiles.Rd ├── getPeptideQuery.Rd ├── getPeptideQuery2.Rd ├── getPeptideScores.Rd ├── getPrecursorByID.Rd ├── getPrecursorSubset.Rd ├── getPrecursors.Rd ├── getPrecursorsQuery.Rd ├── getPrecursorsQueryID.Rd ├── getQuery.Rd ├── getRSE.Rd ├── getRTdf.Rd ├── getRefRun.Rd ├── getRunNames.Rd ├── getSeqSimMatCpp.Rd ├── getTransitions.Rd ├── getTransitionsQuery.Rd ├── getTree.Rd ├── getXICs.Rd ├── getXICs4AlignObj.Rd ├── get_ropenms.Rd ├── imputeChromatogram.Rd ├── mapIdxToTime.Rd ├── mapPrecursorToChromIndices.Rd ├── mappedRTfromAlignObj.Rd ├── masterXICs_DIAlignR.Rd ├── mergeOswAnalytes_ChromHeader.Rd ├── mergeXIC.Rd ├── multipeptide_DIAlignR.Rd ├── nrDesc.Rd ├── oswFiles_DIAlignR.Rd ├── otherChildXICpp.Rd ├── paramsDIAlignR.Rd ├── perBatch.Rd ├── pickNearestFeature.Rd ├── plotAlignedAnalytes.Rd ├── plotAlignmentPath.Rd ├── plotAnalyteXICs.Rd ├── plotSingleAlignedChrom.Rd ├── plotXICgroup.Rd ├── progAlignRuns.Rd ├── progAlignRuns2.Rd ├── readMzMLHeader.Rd ├── readSqMassHeader.Rd ├── recalculateIntensity.Rd ├── script1.Rd ├── script2.Rd ├── setAlignmentRank.Rd ├── sgolayCpp.Rd ├── sgolayFill.Rd ├── smoothSingleXIC.Rd ├── smoothXICs.Rd ├── splineFill.Rd ├── splineFillCpp.Rd ├── traverseDown.Rd ├── traverseUp.Rd ├── trfrParentFeature.Rd ├── trimXICs.Rd ├── uncompressVec.Rd ├── updateFileInfo.Rd ├── updateOnalignTargetedRuns.Rd └── writeTables.Rd ├── python ├── DIAlignPy │ ├── DIAlign.pxd │ ├── PyDIAlign.pyx │ ├── README.md │ ├── setup.py │ ├── test_data.py │ └── test_pydialign.py └── scripts │ └── DIAlignR4win.py ├── src ├── ChromatogramPeak.cpp ├── ChromatogramPeak.h ├── CppInterface.hpp ├── DPosition.cpp ├── DPosition.h ├── MSChromatogram.cpp ├── MSChromatogram.h ├── PeakIntegrator.cpp ├── PeakIntegrator.h ├── RcppExports.cpp ├── Rmain.cpp ├── SavitzkyGolayFilter.cpp ├── SavitzkyGolayFilter.h ├── affinealignment.cpp ├── affinealignment.h ├── affinealignobj.cpp ├── affinealignobj.h ├── alignment.cpp ├── alignment.h ├── chromSimMatrix.cpp ├── chromSimMatrix.h ├── constrainMat.cpp ├── constrainMat.h ├── doc │ └── Doxyfile ├── doc_pages │ ├── Initialization.md │ ├── Matrices.md │ ├── mainpage.md │ ├── nonoverlap.svg │ └── overlap.svg ├── gapPenalty.cpp ├── gapPenalty.h ├── integrateArea.cpp ├── integrateArea.h ├── interface.cpp ├── interface.h ├── miscell.cpp ├── miscell.h ├── peakIntegration │ ├── README.txt │ └── test.cpp ├── run_alignment.cpp ├── similarityMatrix.h ├── simpleFcn.cpp ├── simpleFcn.h ├── spline.cpp ├── spline.h ├── test │ ├── test_affinealignment.cpp │ ├── test_affinealignobj.cpp │ ├── test_alignment.cpp │ ├── test_chromSimMatrix.cpp │ ├── test_constrainMat.cpp │ ├── test_gapPenalty.cpp │ ├── test_integrateArea.cpp │ ├── test_large.tsv │ ├── test_miscell.cpp │ ├── test_simpleFcn.cpp │ ├── test_small.tsv │ └── test_utils.cpp ├── utils.cpp └── utils.h ├── tests ├── testthat.R └── testthat │ ├── test.tsv │ ├── test2.tsv │ ├── test3.tsv │ ├── test_Rmain.R │ ├── test_align_dia_runs.R │ ├── test_chromatogram_manip.R │ ├── test_fill_missing_intensity.R │ ├── test_get_analytes.R │ ├── test_get_filenames.R │ ├── test_get_global_fit.R │ ├── test_get_osw_query.R │ ├── test_get_peaks_chromatograms.R │ ├── test_merge_chromatogram.R │ ├── test_merge_order.R │ ├── test_merge_osw_mzml.R │ ├── test_merge_runs.R │ ├── test_metabo.tsv │ ├── test_pairwise_pep_peak_corp.R │ ├── test_peak_area.R │ ├── test_post_alignment.R │ ├── test_progressive_alignment.R │ ├── test_pyopenms.R │ ├── test_read_mzml.R │ ├── test_read_osw.R │ ├── test_sqMass.R │ └── test_utils.R └── vignettes ├── DIAlignR-vignette.R ├── 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