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

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/DIAlignR.R R/RcppExports.R R/affine_aligned_obj.R R/align_dia_runs.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/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/areaIntegrator.Rd man/chromatogramIdAsInteger.Rd man/constrainSimCpp.Rd man/doAffineAlignmentCpp.Rd man/doAlignmentCpp.Rd man/extractXIC_group.Rd man/fetchAnalytesInfo.Rd man/filenamesFromMZML.Rd man/filenamesFromOSW.Rd man/getAlignObj.Rd man/getAlignObjs.Rd man/getAlignedFigs.Rd man/getAnalytes.Rd man/getAnalytesName.Rd man/getAnalytesQuery.Rd man/getBaseGapPenaltyCpp.Rd man/getChromSimMatCpp.Rd man/getGlobalAlignMaskCpp.Rd man/getGlobalAlignment.Rd man/getLOESSfit.Rd man/getLinearfit.Rd man/getMZMLpointers.Rd man/getMappedRT.Rd man/getOswAnalytes.Rd man/getOswFiles.Rd man/getQuery.Rd man/getRefRun.Rd man/getRunNames.Rd man/getSeqSimMatCpp.Rd man/getXICs.Rd man/getXICs4AlignObj.Rd man/mapIdxToTime.Rd man/mappedRTfromAlignObj.Rd man/mergeOswAnalytes_ChromHeader.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/selectChromIndices.Rd
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/gapPenalty.cpp
src/gapPenalty.h
src/integrateArea.cpp
src/integrateArea.h
src/interface.cpp
src/interface.h
src/similarityMatrix.h
src/simpleFcn.cpp
src/simpleFcn.h
src/utils.cpp
src/utils.h
tests/testthat.R tests/testthat/test_Rmain.R tests/testthat/test_align_dia_runs.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.Rmd
vignettes/DIAlignR.bib
shubham1637/DIAlign documentation built on Feb. 6, 2020, 8:15 a.m.