Files in DIAlignR

Dynamic Programming Based Alignment of MS2 Chromatograms

README.md R/read_mzml.R R/get_filenames.R R/affine_aligned_obj.R R/get_osw_query.R R/RcppExports.R R/utils.R R/read_osw.R R/DIAlignR.R R/align_dia_runs.R R/chromatogram_manip.R R/pairwise_pep_peak_corp.R R/data.R R/get_peaks_chromatograms.R R/merge_osw_mzml.R R/post_alignment.R R/get_analytes.R R/get_global_fit.R R/visualise_chromatograms.R vignettes/DIAlignR-vignette.Rmd man/getFeatures.Rd man/plotAlignmentPath.Rd man/DIAlignR.Rd man/getGlobalAlignment.Rd man/mapPrecursorToChromIndices.Rd man/getChromSimMatCpp.Rd man/getPrecursorByID.Rd man/filenamesFromOSW.Rd man/constrainSimCpp.Rd man/mappedRTfromAlignObj.Rd man/smoothSingleXIC.Rd man/getPrecursors.Rd man/AffineAlignObjLight-class.Rd man/extractXIC_group.Rd man/getLinearfit.Rd man/getAlignObj.Rd man/getPrecursorsQuery.Rd man/getQuery.Rd man/areaIntegrator.Rd man/oswFiles_DIAlignR.Rd man/fetchPrecursorsInfo.Rd man/getGlobalFits.Rd man/as.list-AffineAlignObj-method.Rd man/as.list-AffineAlignObjMedium-method.Rd man/AffineAlignObj-class.Rd man/getXICs.Rd man/doAffineAlignmentCpp.Rd man/getPrecursorsQueryID.Rd man/writeTables.Rd man/alignTargetedRuns.Rd man/updateFileInfo.Rd man/as.list-AlignObj-method.Rd man/analytesFromFeatures.Rd man/doAlignmentCpp.Rd man/getFeaturesQuery.Rd man/getBaseGapPenaltyCpp.Rd man/getAlignedIndices.Rd man/chromatogramIdAsInteger.Rd man/mapIdxToTime.Rd man/getOswAnalytes.Rd man/getMappedRT.Rd man/as.list-AffineAlignObjLight-method.Rd man/smoothXICs.Rd man/pickNearestFeature.Rd man/AffineAlignObjMedium-class.Rd man/plotSingleAlignedChrom.Rd man/readChromatogramHeader.Rd man/setAlignmentRank.Rd man/calculateIntensity.Rd man/fetchFeaturesFromRun.Rd man/getChromatogramIndices.Rd man/fetchAnalytesInfo.Rd man/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.Rd man/getLOESSfit.Rd man/plotXICgroup.Rd man/getOswFiles.Rd man/getAnalytesQuery.Rd man/getXICs4AlignObj.Rd man/plotAnalyteXICs.Rd man/getAlignObjs.Rd man/getGlobalAlignMaskCpp.Rd man/getRunNames.Rd man/filenamesFromMZML.Rd man/multipeptide_DIAlignR.Rd man/getSeqSimMatCpp.Rd man/alignChromatogramsCpp.Rd man/getRefRun.Rd man/mergeOswAnalytes_ChromHeader.Rd man/plotAlignedAnalytes.Rd man/getMultipeptide.Rd man/getRSE.Rd man/getMZMLpointers.Rd man/AlignObj-class.Rd man/getAlignedFigs.Rd man/trimXICs.Rd tests/testthat.R tests/testthat/test_get_filenames.R tests/testthat/test_Rmain.R tests/testthat/test_get_peaks_chromatograms.R tests/testthat/test_read_mzml.R tests/testthat/test_read_osw.R tests/testthat/test_get_analytes.R tests/testthat/test_post_alignment.R tests/testthat/test_get_global_fit.R tests/testthat/test_align_dia_runs.R tests/testthat/test_pairwise_pep_peak_corp.R tests/testthat/test_merge_osw_mzml.R tests/testthat/test_get_osw_query.R tests/testthat/test_utils.R tests/testthat/test_chromatogram_manip.R inst/doc/DIAlignR-vignette.Rmd inst/doc/DIAlignR-vignette.R