# Dynamic Programming Based Alignment of MS2 Chromatograms

## Documentation for package ‘DIAlignR’ version 2.8.0

- 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
alignObj_DIAlignR | Alignment object of a peptide.
alignTargetedRuns | Outputs intensities for each analyte from aligned Targeted-MS runs
alignToRoot4 | Step 4 for progressive alignment
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
childXICs | Get child chromatograms from parents
constrainSimCpp | Constrain similarity matrix with a mask
createMZML | Create an mzML file
createSqMass | Create an sqMass file
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
getAlignedTimes | Get aligned Retention times.
getAlignedTimesCpp | Get aligned indices from MS2 extracted-ion chromatograms(XICs) pair.
getAlignedTimesFast | 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.
getChildXICpp | Get child chromatogram from two parent chromatogram
getChildXICs | Develop child XICs for precursors
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.
getNativeIDs | Fetch NativeIDs
getPeptideScores | Get scores of peptide
getPrecursorByID | Find precursors given their IDs
getPrecursorIndices | Get MS1 chromatogram indices of precursors.
getPrecursors | Get precursors from all feature files
getRefExpFeatureMap | Alignment Feature Mapping Table
getRefRun | Fetch the reference run for each peptide
getRTdf | Calculates global alignment between RT of two runs
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
mstAlignRuns | Peptide quantification through MST alignment
mstScript1 | Extract features and generate minimum spanning tree.
mstScript2 | Performs alignment using mstScript1 output
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
reduceXICs | Subset an XIC file
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
XIC_QFNNTDIVLLEDFQK_3_DIAlignR | Extracted-ion chromatograms (XICs) of a peptide