Files in shubham1637/DIAlignR
Dynamic Programming Based Alignment of MS2 Chromatograms

.Rbuildignore
.gitignore
.travis.yml
CMakeLists.txt
DESCRIPTION
DIAlignR.Rproj
NAMESPACE
NEWS
R/DIAlignR.R R/RcppExports.R R/affine_aligned_obj.R R/align_dia_runs.R R/chromatogram_manip.R R/data.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_osw_mzml.R R/pairwise_pep_peak_corp.R R/post_alignment.R R/read_mzml.R R/read_osw.R R/utils.R R/visualise_chromatograms.R README.md
TODO
data-raw/test_GenerateChroms.txt
data-raw/test_GenerateData.R
data/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.rda
data/multipeptide_DIAlignR.rda
data/oswFiles_DIAlignR.rda
inst/buildDIAlignR.txt
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
man/AffineAlignObj-class.Rd man/AffineAlignObjLight-class.Rd man/AffineAlignObjMedium-class.Rd man/AlignObj-class.Rd man/DIAlignR.Rd man/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.Rd man/alignChromatogramsCpp.Rd man/alignTargetedRuns.Rd man/analytesFromFeatures.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/calculateIntensity.Rd man/chromatogramIdAsInteger.Rd man/constrainSimCpp.Rd man/doAffineAlignmentCpp.Rd man/doAlignmentCpp.Rd man/extractXIC_group.Rd man/fetchAnalytesInfo.Rd man/fetchFeaturesFromRun.Rd man/fetchPrecursorsInfo.Rd man/filenamesFromMZML.Rd man/filenamesFromOSW.Rd man/getAlignObj.Rd man/getAlignObjs.Rd man/getAlignedFigs.Rd man/getAlignedIndices.Rd man/getAnalytesQuery.Rd man/getBaseGapPenaltyCpp.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/getMZMLpointers.Rd man/getMappedRT.Rd man/getMultipeptide.Rd man/getOswAnalytes.Rd man/getOswFiles.Rd man/getPrecursorByID.Rd man/getPrecursors.Rd man/getPrecursorsQuery.Rd man/getPrecursorsQueryID.Rd man/getQuery.Rd man/getRSE.Rd man/getRefRun.Rd man/getRunNames.Rd man/getSeqSimMatCpp.Rd man/getXICs.Rd man/getXICs4AlignObj.Rd man/mapIdxToTime.Rd man/mapPrecursorToChromIndices.Rd man/mappedRTfromAlignObj.Rd man/mergeOswAnalytes_ChromHeader.Rd man/multipeptide_DIAlignR.Rd man/oswFiles_DIAlignR.Rd man/pickNearestFeature.Rd man/plotAlignedAnalytes.Rd man/plotAlignmentPath.Rd man/plotAnalyteXICs.Rd man/plotSingleAlignedChrom.Rd man/plotXICgroup.Rd man/readChromatogramHeader.Rd man/setAlignmentRank.Rd man/smoothSingleXIC.Rd man/smoothXICs.Rd man/trimXICs.Rd man/updateFileInfo.Rd man/writeTables.Rd
python/DIAlignPy/DIAlign.pxd
python/DIAlignPy/PyDIAlign.pyx
python/DIAlignPy/README.md
python/DIAlignPy/setup.py
python/DIAlignPy/test_data.py
python/DIAlignPy/test_pydialign.py
python/scripts/DIAlignR4win.py
src/ChromatogramPeak.cpp
src/ChromatogramPeak.h
src/CppInterface.hpp
src/DPosition.cpp
src/DPosition.h
src/MSChromatogram.cpp
src/MSChromatogram.h
src/PeakIntegrator.cpp
src/PeakIntegrator.h
src/RcppExports.cpp
src/Rmain.cpp
src/affinealignment.cpp
src/affinealignment.h
src/affinealignobj.cpp
src/affinealignobj.h
src/alignment.cpp
src/alignment.h
src/chromSimMatrix.cpp
src/chromSimMatrix.h
src/constrainMat.cpp
src/constrainMat.h
src/doc/Doxyfile
src/doc_pages/Initialization.md src/doc_pages/Matrices.md src/doc_pages/mainpage.md
src/doc_pages/nonoverlap.svg
src/doc_pages/overlap.svg
src/gapPenalty.cpp
src/gapPenalty.h
src/integrateArea.cpp
src/integrateArea.h
src/interface.cpp
src/interface.h
src/peakIntegration/README.txt
src/peakIntegration/test.cpp
src/run_alignment.cpp
src/similarityMatrix.h
src/simpleFcn.cpp
src/simpleFcn.h
src/test/test_affinealignment.cpp
src/test/test_affinealignobj.cpp
src/test/test_alignment.cpp
src/test/test_chromSimMatrix.cpp
src/test/test_constrainMat.cpp
src/test/test_gapPenalty.cpp
src/test/test_integrateArea.cpp
src/test/test_large.tsv
src/test/test_simpleFcn.cpp
src/test/test_small.tsv
src/test/test_utils.cpp
src/utils.cpp
src/utils.h
tests/testthat.R
tests/testthat/test.csv
tests/testthat/test2.csv
tests/testthat/test_Rmain.R tests/testthat/test_align_dia_runs.R tests/testthat/test_chromatogram_manip.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_osw_mzml.R tests/testthat/test_pairwise_pep_peak_corp.R tests/testthat/test_post_alignment.R tests/testthat/test_read_mzml.R tests/testthat/test_read_osw.R tests/testthat/test_utils.R vignettes/DIAlignR-vignette.R vignettes/DIAlignR-vignette.Rmd
vignettes/DIAlignR-vignette.html
vignettes/DIAlignR.bib
shubham1637/DIAlignR documentation built on May 15, 2020, 3:28 a.m.