Dynamic Programming Based Alignment of MS2 Chromatograms

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Documentation for package ‘DIAlignR’ version 2.7.0

• 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
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