AffineAlignObj-class    An S4 object for class AffineAlignObj
AffineAlignObjLight-class
                        An S4 object for class AffineAlignObjLight It
                        only contains aligned indices.
AffineAlignObjMedium-class
                        An S4 object for class AffineAlignObjMedium. 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.
as.list,AffineAlignObj-method
                        Converts instances of class AffineAlignObj into
                        list
as.list,AffineAlignObjLight-method
                        Converts instances of class AffineAlignObjLight
                        into list
as.list,AffineAlignObjMedium-method
                        Converts instances of class
                        AffineAlignObjMedium into list
as.list,AlignObj-method
                        Converts instances of class AlignObj into list
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
getAlignedIndices       Get aligned Retention times.
getBaseGapPenaltyCpp    Calculates gap penalty for dynamic programming
                        based alignment.
getChromSimMatCpp       Calculates similarity matrix of two
                        fragment-ion chromatogram groups or
                        extracted-ion chromatograms(XICs)
getChromatogramIndices
                        Get chromatogram indices of precursors.
getFeatures             Get features from all feature files
getGlobalAlignMaskCpp   Outputs a mask for constraining similarity
                        matrix
getGlobalAlignment      Calculates global alignment between RT of two
                        runs
getMZMLpointers         Get pointers to each mzML file.
getMultipeptide         Get multipeptides
getPrecursorByID        Find precursors given their IDs
getPrecursors           Get precursors from all feature files
getRunNames             Get names of all runs
getSeqSimMatCpp         Calculates similarity matrix for two sequences
getXICs                 Get XICs of all analytes
getXICs4AlignObj        Extract XICs of analytes
mapIdxToTime            Establishes mapping from index to time
multipeptide_DIAlignR   Analytes information from multipeptide.
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
trimXICs                Selects a part of chromatograms
updateFileInfo          Get intersection of runs and fileInfo
