Dynamic Programming Based Alignment of MS2 Chromatograms

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Documentation for package ‘DIAlignR’ version 0.99.12

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DIAlignR-package DIAlignR
AffineAlignObj An S4 object for class AffineAlignObj
AffineAlignObj-class An S4 object for class AffineAlignObj
AffineAlignObjLight An S4 object for class AffineAlignObj. It only contains aligned indices.
AffineAlignObjLight-class An S4 object for class AffineAlignObj. It only contains aligned indices.
AffineAlignObjMedium An S4 object for class AffineAlignObj. It only contains similarity matrix and aligned indices.
AffineAlignObjMedium-class An S4 object for class AffineAlignObj. It only contains similarity matrix and aligned indices.
alignChromatogramsCpp Aligns MS2 extracted-ion chromatograms(XICs) pair.
AlignObj An S4 object for class AlignObj
AlignObj-class An S4 object for class AlignObj
alignTargetedRuns Outputs intensities for each analyte from aligned Targeted-MS runs
areaIntegrator Calculates area between signal-boundaries.
constrainSimCpp Constrain similarity matrix with a mask
DIAlignR DIAlignR
doAffineAlignmentCpp Perform affine global and overlap alignment on a similarity matrix
doAlignmentCpp Perform non-affine global and overlap alignment on a similarity matrix
getAlignObj Outputs AlignObj from an alignment of two XIC-groups
getAlignObjs AlignObj for analytes between a pair of runs
getAnalytes Get names of analytes found in all runs.
getBaseGapPenaltyCpp Calculates gap penalty for dynamic programming based alignment.
getChromSimMatCpp Calculates similarity matrix of two fragment-ion chromatogram groups or extracted-ion chromatograms(XICs)
getGlobalAlignMaskCpp Outputs a mask for constraining similarity matrix
getGlobalAlignment Calculates global alignment between RT of two runs
getMappedRT Get mapping of reference RT on experiment run.
getMZMLpointers Get pointers to each mzML file.
getOswAnalytes Fetch analytes from OSW file
getOswFiles Get list of peptides and their chromatogram indices.
getRunNames Get names of all runs
getSeqSimMatCpp Calculates similarity matrix for two sequences
getXICs Get XICs of all analytes
getXICs4AlignObj Extract XICs of all analytes from oswFiles
mapIdxToTime Establishes mapping from index to time
oswFiles_DIAlignR Analytes information from osw files
plotAlignedAnalytes Plot aligned XICs group for a specific peptide. AlignObjOutput is the output from getAlignObjs fucntion.
plotAlignmentPath Visualize alignment path through similarity matrix
plotAnalyteXICs Plot extracted-ion chromatogram.
plotXICgroup Plot Extracted-ion chromatogram group.
smoothSingleXIC Smooth chromatogram signal
smoothXICs Smooth chromatogram signals from a list
XIC_QFNNTDIVLLEDFQK_3_DIAlignR Extracted-ion chromatograms (XICs) of a peptide