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| AffineAlignObj | An S4 object for class AffineAlignObj |
| AffineAlignObj-class | An S4 object for class AffineAlignObj |
| AffineAlignObjLight | An S4 object for class AffineAlignObjLight It only contains aligned indices. |
| AffineAlignObjLight-class | An S4 object for class AffineAlignObjLight It only contains aligned indices. |
| AffineAlignObjMedium | An S4 object for class AffineAlignObjMedium. It only contains similarity matrix and aligned indices. |
| AffineAlignObjMedium-class | An S4 object for class AffineAlignObjMedium. 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. |
| as.list-method | Converts instances of class AffineAlignObj into list |
| as.list-method | Converts instances of class AffineAlignObjLight into list |
| as.list-method | Converts instances of class AffineAlignObjMedium into list |
| as.list-method | Converts instances of class AlignObj into list |
| 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 |
| getAlignedIndices | Get aligned Retention times. |
| getAlignObj | Outputs AlignObj from an alignment of two XIC-groups |
| getAlignObjs | AlignObj for analytes between a pair of runs |
| getBaseGapPenaltyCpp | Calculates gap penalty for dynamic programming based alignment. |
| getChromatogramIndices | Get chromatogram indices of precursors. |
| getChromSimMatCpp | Calculates similarity matrix of two fragment-ion chromatogram groups or extracted-ion chromatograms(XICs) |
| getFeatures | Get features from all feature files |
| getGlobalAlignMaskCpp | Outputs a mask for constraining similarity matrix |
| getGlobalAlignment | Calculates global alignment between RT of two runs |
| getMultipeptide | Get multipeptides |
| getMZMLpointers | Get pointers to each mzML file. |
| 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 |
| XIC_QFNNTDIVLLEDFQK_3_DIAlignR | Extracted-ion chromatograms (XICs) of a peptide |