AffineAlignObj-class    An S4 object for class AffineAlignObj
AffineAlignObjLight-class
                        An S4 object for class AffineAlignObj. It only
                        contains aligned indices.
AffineAlignObjMedium-class
                        An S4 object for class AffineAlignObj. It only
                        contains similarity matrix and aligned indices.
AlignObj-class          An S4 object for class AlignObj
DIAlignR                DIAlignR
XIC_QFNNTDIVLLEDFQK_3_DIAlignR
                        Extracted-ion chromatograms (XICs) of a peptide
alignChromatogramsCpp   Aligns MS2 extracted-ion chromatograms(XICs)
                        pair.
alignTargetedRuns       Outputs intensities for each analyte from
                        aligned Targeted-MS runs
areaIntegrator          Calculates area between signal-boundaries.
constrainSimCpp         Constrain similarity matrix with a mask
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
getMZMLpointers         Get pointers to each mzML file.
getMappedRT             Get mapping of reference RT on experiment run.
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
