Man pages for shubham1637/DIAlign
Dynamic Programming Based Alignment of MS2 Chromatograms

AffineAlignObj-classAn S4 object for class AffineAlignObj
AffineAlignObjLight-classAn S4 object for class AffineAlignObj. It only contains...
AffineAlignObjMedium-classAn S4 object for class AffineAlignObj. It only contains...
alignChromatogramsCppAligns MS2 extracted-ion chromatograms(XICs) pair.
AlignObj-classAn S4 object for class AlignObj
alignTargetedRunsOutputs intensities for each analyte from aligned Targeted-MS...
areaIntegratorCalculates area between signal-boundaries.
chromatogramIdAsIntegerCoerce chromatogram ids as integer
constrainSimCppConstrain similarity matrix with a mask
doAffineAlignmentCppPerform affine global and overlap alignment on a similarity...
doAlignmentCppPerform non-affine global and overlap alignment on a...
extractXIC_groupExtract XICs of all transitions requested in chromIndices.
fetchAnalytesInfoFetch features of analytes
filenamesFromMZMLGet mzML filenames from the directory.
filenamesFromOSWGet mzML filenames from osw RUN table.
getAlignedFigsPlot aligned XICs group for a specific peptide.
getAlignObjOutputs AlignObj from an alignment of two XIC-groups
getAlignObjsAlignObj for analytes between a pair of runs
getAnalytesGet names of analytes found in all runs.
getAnalytesNameGet names of analytes found in all runs
getAnalytesQueryGenerate SQL query to fetch limited information from osw...
getBaseGapPenaltyCppCalculates gap penalty for dynamic programming based...
getChromSimMatCppCalculates similarity matrix of two fragment-ion chromatogram...
getGlobalAlignMaskCppOutputs a mask for constraining similarity matrix
getGlobalAlignmentCalculates global alignment between RT of two runs
getLinearfitCalculates linear fit between RT of two runs
getLOESSfitCalculates LOESS fit between RT of two runs
getMappedRTGet mapping of reference RT on experiment run.
getMZMLpointersGet pointers to each mzML file.
getOswAnalytesFetch analytes from OSW file
getOswFilesGet list of peptides and their chromatogram indices.
getQueryGenerate SQL query to fetch information from osw files.
getRefRunFetch the reference run-index.
getRunNamesGet names of all runs
getSeqSimMatCppCalculates similarity matrix for two sequences
getXICsGet XICs of all analytes
getXICs4AlignObjExtract XICs of all analytes from oswFiles
mapIdxToTimeEstablishes mapping from index to time
mappedRTfromAlignObjMap reference run time on the experiment run.
mergeOswAnalytes_ChromHeaderMerge dataframes from OSW and mzML files
oswFiles_DIAlignRAnalytes information from osw files
pickNearestFeaturePick feature closest to reference peak
plotAlignedAnalytesPlot aligned XICs group for a specific peptide....
plotAlignmentPathVisualize alignment path through similarity matrix
plotAnalyteXICsPlot extracted-ion chromatogram.
plotSingleAlignedChromPlot an aligned XIC-group.
plotXICgroupPlot Extracted-ion chromatogram group.
readChromatogramHeaderGet chromatogram header from a mzML file
selectChromIndicesChromatogram indices of analyte in a run.
XIC_QFNNTDIVLLEDFQK_3_DIAlignRExtracted-ion chromatograms (XICs) of a peptide
shubham1637/DIAlign documentation built on Feb. 6, 2020, 8:15 a.m.