Dynamic Programming Based Alignment of MS2 Chromatograms


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Documentation for package ‘DIAlignR’ version 2.8.0

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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
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