Files in shubham1637/DIAlignR

Dynamic Programming Based Alignment of MS2 Chromatograms

R/DIAlignR.R R/RcppExports.R R/affine_aligned_obj.R R/align_dia_runs.R R/chromatogram_manip.R R/data.R R/fill_missing_intensity.R R/get_analytes.R R/get_filenames.R R/get_global_fit.R R/get_osw_query.R R/get_peaks_chromatograms.R R/merge_chromatogram.R R/merge_order.R R/merge_osw_mzml.R R/merge_runs.R R/mstAlign.R R/nature_paper.R R/pairwise_pep_peak_corp.R R/peak_area.R R/post_alignment.R R/progressive_alignment.R R/pyopenms.R R/read_mzml.R R/read_osw.R R/reduce_files.R R/scripts.R R/sqMass.R R/utils.R R/visualise_chromatograms.R README.md Rscript/alignTargetedRuns_cli.R data-raw/test_GenerateData.R man/AffineAlignObj-class.Rd man/AffineAlignObjLight-class.Rd man/AffineAlignObjMedium-class.Rd man/AlignObj-class.Rd man/DIAlignR.Rd man/MSTperBatch.Rd man/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.Rd man/addFlankToLeft.Rd man/addFlankToRight.Rd man/addXIC.Rd man/alignChromatogramsCpp.Rd man/alignObj_DIAlignR.Rd man/alignTargetedRuns.Rd man/alignToMaster.Rd man/alignToRef.Rd man/alignToRefMST.Rd man/alignToRoot4.Rd man/alignedXIC.Rd man/alignmentStats.Rd man/analytesFromFeatures.Rd man/approxFill.Rd man/areaIntegrator.Rd man/as.list-AffineAlignObj-method.Rd man/as.list-AffineAlignObjLight-method.Rd man/as.list-AffineAlignObjMedium-method.Rd man/as.list-AlignObj-method.Rd man/blobXICs.Rd man/calculateIntensity.Rd man/checkOverlap.Rd man/checkParams.Rd man/childXIC.Rd man/childXICs.Rd man/chromatogramIdAsInteger.Rd man/constrainSimCpp.Rd man/createMZML.Rd man/createSqMass.Rd man/dialignrLoess.Rd man/doAffineAlignmentCpp.Rd man/doAlignmentCpp.Rd man/extractXIC_group.Rd man/extractXIC_group2.Rd man/fetchAnalytesInfo.Rd man/fetchFeaturesFromRun.Rd man/fetchPeptidesInfo.Rd man/fetchPeptidesInfo2.Rd man/fetchPrecursorsInfo.Rd man/fetchTransitionsFromRun.Rd man/filenamesFromMZML.Rd man/filenamesFromOSW.Rd man/getAlignObj.Rd man/getAlignObjs.Rd man/getAlignedFigs.Rd man/getAlignedIndices.Rd man/getAlignedTimes.Rd man/getAlignedTimesCpp.Rd man/getAlignedTimesFast.Rd man/getAnalytesQuery.Rd man/getBaseGapPenaltyCpp.Rd man/getChildFeature.Rd man/getChildXICpp.Rd man/getChildXICs.Rd man/getChromSimMatCpp.Rd man/getChromatogramIndices.Rd man/getFeatures.Rd man/getFeaturesQuery.Rd man/getGlobalAlignMaskCpp.Rd man/getGlobalAlignment.Rd man/getGlobalFits.Rd man/getLOESSfit.Rd man/getLinearfit.Rd man/getMST.Rd man/getMZMLpointers.Rd man/getMappedRT.Rd man/getMultipeptide.Rd man/getNativeIDs.Rd man/getNodeIDs.Rd man/getNodeRun.Rd man/getOswAnalytes.Rd man/getOswFiles.Rd man/getPeptideQuery.Rd man/getPeptideQuery2.Rd man/getPeptideScores.Rd man/getPrecursorByID.Rd man/getPrecursorIndices.Rd man/getPrecursorSubset.Rd man/getPrecursors.Rd man/getPrecursorsQuery.Rd man/getPrecursorsQueryID.Rd man/getQuery.Rd man/getRSE.Rd man/getRTdf.Rd man/getRefExpFeatureMap.Rd man/getRefRun.Rd man/getRunNames.Rd man/getSeqSimMatCpp.Rd man/getTransitions.Rd man/getTransitionsQuery.Rd man/getTree.Rd man/getXICs.Rd man/getXICs4AlignObj.Rd man/get_ropenms.Rd man/imputeChromatogram.Rd man/ipfReassignFDR.Rd man/mapIdxToTime.Rd man/mapPrecursorToChromIndices.Rd man/mappedRTfromAlignObj.Rd man/masterXICs_DIAlignR.Rd man/mergeOswAnalytes_ChromHeader.Rd man/mergeXIC.Rd man/mstAlignRuns.Rd man/mstScript1.Rd man/mstScript2.Rd man/multipeptide_DIAlignR.Rd man/nrDesc.Rd man/oswFiles_DIAlignR.Rd man/otherChildXICpp.Rd man/paramsDIAlignR.Rd man/perBatch.Rd man/pickNearestFeature.Rd man/plotAlignedAnalytes.Rd man/plotAlignmentPath.Rd man/plotAnalyteXICs.Rd man/plotSingleAlignedChrom.Rd man/plotXICgroup.Rd man/populateReferenceExperimentFeatureAlignmentMap.Rd man/progAlignRuns.Rd man/progComb3.Rd man/progSplit2.Rd man/progSplit4.Rd man/progTree1.Rd man/readMzMLHeader.Rd man/readSqMassHeader.Rd man/recalculateIntensity.Rd man/reduceXICs.Rd man/script1.Rd man/script2.Rd man/setAlignmentRank.Rd man/sgolayCpp.Rd man/sgolayFill.Rd man/smoothSingleXIC.Rd man/smoothXICs.Rd man/splineFill.Rd man/splineFillCpp.Rd man/traverseDown.Rd man/traverseMST.Rd man/traverseUp.Rd man/trfrParentFeature.Rd man/trimXICs.Rd man/uncompressVec.Rd man/updateFileInfo.Rd man/updateOnalignTargetedRuns.Rd man/writeOutFeatureAlignmentMap.Rd man/writeTables.Rd python/DIAlignPy/README.md src/doc_pages/Initialization.md src/doc_pages/Matrices.md src/doc_pages/mainpage.md tests/testthat.R tests/testthat/test_Rmain.R tests/testthat/test_align_dia_runs.R tests/testthat/test_chromatogram_manip.R tests/testthat/test_fill_missing_intensity.R tests/testthat/test_get_analytes.R tests/testthat/test_get_filenames.R tests/testthat/test_get_global_fit.R tests/testthat/test_get_osw_query.R tests/testthat/test_get_peaks_chromatograms.R tests/testthat/test_merge_chromatogram.R tests/testthat/test_merge_order.R tests/testthat/test_merge_osw_mzml.R tests/testthat/test_merge_runs.R tests/testthat/test_mstAlign.R tests/testthat/test_pairwise_pep_peak_corp.R tests/testthat/test_peak_area.R tests/testthat/test_post_alignment.R tests/testthat/test_progressive_alignment.R tests/testthat/test_pyopenms.R tests/testthat/test_read_mzml.R tests/testthat/test_read_osw.R tests/testthat/test_sqMass.R tests/testthat/test_utils.R vignettes/DIAlignR-vignette.R vignettes/DIAlignR-vignette.Rmd