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.
alignObj_DIAlignR       Alignment object of a peptide.
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
childXICs               Get child chromatograms from parents
constrainSimCpp         Constrain similarity matrix with a mask
createMZML              Create an mzML file
createSqMass            Create an sqMass file
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
getAlignedTimes         Get aligned Retention times.
getAlignedTimesCpp      Get aligned indices from MS2 extracted-ion
                        chromatograms(XICs) pair.
getAlignedTimesFast     Get aligned Retention times.
getBaseGapPenaltyCpp    Calculates gap penalty for dynamic programming
                        based alignment.
getChildXICpp           Get child chromatogram from two parent
                        chromatogram
getChildXICs            Develop child XICs for precursors
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
getPeptideScores        Get scores of peptide
getPrecursorByID        Find precursors given their IDs
getPrecursors           Get precursors from all feature files
getRTdf                 Calculates global alignment between RT of two
                        runs
getRefRun               Fetch the reference run for each peptide
getRunNames             Get names of all runs
getSeqSimMatCpp         Calculates similarity matrix for two sequences
getTransitions          Get transitions from all feature files
getXICs                 Get XICs of all analytes
getXICs4AlignObj        Extract XICs of analytes
get_ropenms             Get ropenms handle
imputeChromatogram      Fill missing intensities in a chromatogram
mapIdxToTime            Establishes mapping from index to time
masterXICs_DIAlignR     Master fragment-ion chromatograms from two
                        parents
multipeptide_DIAlignR   Analytes information from multipeptide.
oswFiles_DIAlignR       Analytes information from osw files
otherChildXICpp         Get child chromatogram for other precursors
                        using main precursor alignment
paramsDIAlignR          Parameters for the alignment functions
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.
progAlignRuns           Peptide quantification through progressive
                        alignment
progComb3               Step 3 for progressive alignment
progSplit2              Step 2 for progressive alignment
progSplit4              Step 4 for progressive alignment
progTree1               Step 1 for progressive alignment
recalculateIntensity    Calculates area of peaks in peakTable
script1                 Extract features and generate pairwise
                        alignments.
script2                 Performs alignment using script1 output
sgolayCpp               Smooth chromatogram with savitzky-golay filter.
smoothSingleXIC         Smooth chromatogram signal
smoothXICs              Smooth chromatogram signals from a list
splineFillCpp           Interpolate using spline
trimXICs                Selects a part of chromatograms
updateFileInfo          Get intersection of runs and fileInfo
