Files in DIAlignR

Dynamic Programming Based Alignment of MS2 Chromatograms

README.md

NEWS

NAMESPACE

DESCRIPTION

src/alignment.h

src/chromSimMatrix.h

src/DPosition.h

src/utils.cpp

src/MSChromatogram.cpp

src/gapPenalty.h

src/interface.h

src/RcppExports.cpp

src/alignment.cpp

src/integrateArea.h

src/constrainMat.cpp

src/affinealignment.h

src/ChromatogramPeak.h

src/constrainMat.h

src/affinealignobj.cpp

src/integrateArea.cpp

src/ChromatogramPeak.cpp

src/similarityMatrix.h

src/interface.cpp

src/simpleFcn.cpp

src/PeakIntegrator.cpp

src/Rmain.cpp

src/PeakIntegrator.h

src/affinealignment.cpp

src/chromSimMatrix.cpp

src/DPosition.cpp

src/affinealignobj.h

src/MSChromatogram.h

src/utils.h

src/simpleFcn.h

src/gapPenalty.cpp

src/peakIntegration/README.txt

src/peakIntegration/test.cpp

data/oswFiles_DIAlignR.rda

data/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.rda

data/multipeptide_DIAlignR.rda

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

vignettes/DIAlignR.bib

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/test2.csv

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.csv

tests/testthat/test_utils.R tests/testthat/test_chromatogram_manip.R

inst/buildDIAlignR.txt

inst/doc/DIAlignR-vignette.Rmd

inst/doc/DIAlignR-vignette.html

inst/doc/DIAlignR-vignette.R

inst/extdata/mzml/hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt.chrom.mzML

inst/extdata/mzml/hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML

inst/extdata/mzml/hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML

inst/extdata/osw/merged.osw

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.