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 |