# Dynamic Programming Based Alignment of MS2 Chromatograms

## Documentation for package ‘DIAlignR’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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