Man pages for Roestlab/DIAlignR
Dynamic Programming Based Alignment of MS2 Chromatograms
| addFlankToLeft | Add signal to the left of XIC |
| addFlankToRight | Add signal to the right of XIC |
| addXIC | Add XIC to pyopenms experiment |
| AffineAlignObj-class | An S4 object for class AffineAlignObj |
| AffineAlignObjLight-class | An S4 object for class AffineAlignObjLight It only contains... |
| AffineAlignObjMedium-class | An S4 object for class AffineAlignObjMedium. It only contains... |
| alignChromatogramsCpp | Aligns MS2 extracted-ion chromatograms(XICs) pair. |
| alignedXIC | Create an aligned chromatogram |
| alignmentStats | Prints alignment summary |
| 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... |
| alignTargetedRuns2 | Star alignment for few ids |
| alignToMaster | Align descendants to master |
| alignToRef | Aligns an analyte from an experiment to the reference run |
| analytesFromFeatures | Outputs analytes below FDR |
| approxFill | Fill missing values using linear interpolation |
| areaIntegrator | Calculates area between signal-boundaries. |
| as.list-AffineAlignObjLight-method | Converts instances of class AffineAlignObjLight into list |
| as.list-AffineAlignObjMedium-method | Converts instances of class AffineAlignObjMedium into list |
| as.list-AffineAlignObj-method | Converts instances of class AffineAlignObj into list |
| as.list-AlignObj-method | Converts instances of class AlignObj into list |
| blobXICs | Format XICs to blob |
| calculateIntensity | Calculates area of a peak in XIC group |
| checkOverlap | Overlap of two time ranges |
| checkParams | Checks all the alignment parameters |
| childXIC | Get a child chromatogram from parents |
| childXICs | Get child chromatograms from parents |
| chromatogramIdAsInteger | Coerce chromatogram ids as integer |
| constrainSimCpp | Constrain similarity matrix with a mask |
| createMZML | Create an mzML file |
| createSqMass | Create an sqMass file |
| DIAlignR | DIAlignR |
| dialignrLoess | Modified loess for condition handling |
| doAffineAlignmentCpp | Perform affine global and overlap alignment on a similarity... |
| doAlignmentCpp | Perform non-affine global and overlap alignment on a... |
| extractXIC_group | Extract XICs of chromIndices |
| extractXIC_group2 | Extract XICs of chromIndices |
| fetchAnalytesInfo | Fetch features of analytes |
| fetchFeaturesFromRun | Get features from a feature file. |
| fetchPeptidesInfo | Get scores of all peptides |
| fetchPeptidesInfo2 | Get scores of all peptides |
| fetchPrecursorsInfo | Get precursors from a feature file |
| fetchTransitionsFromRun | Get transitions from a feature file |
| filenamesFromMZML | Get mzML filenames from the directory. |
| filenamesFromOSW | Get mzML filenames from osw RUN table. |
| getAlignedFigs | Plot aligned XICs group for a specific peptide. |
| getAlignedIndices | Get aligned indices. |
| getAlignedTimes | Get aligned Retention times. |
| getAlignedTimesCpp | Get aligned indices from MS2 extracted-ion... |
| getAlignedTimesFast | Get aligned Retention times. |
| getAlignObj | Outputs AlignObj from an alignment of two XIC-groups |
| getAlignObjs | AlignObj for analytes between a pair of runs |
| getAnalytesQuery | Generate SQL query to fetch limited information from osw... |
| getBaseGapPenaltyCpp | Calculates gap penalty for dynamic programming based... |
| getChildFeature | Transform features to child time-domain |
| 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... |
| getFeatures | Get features from all feature files |
| getFeaturesQuery | Get features from a SQLite file |
| getGlobalAlignMaskCpp | Outputs a mask for constraining similarity matrix |
| getGlobalAlignment | Calculates global alignment between RT of two runs |
| getGlobalFits | Calculates all global alignment needed in refRun |
| getLinearfit | Calculates linear fit between RT of two runs |
| getLOESSfit | Calculates LOESS fit between RT of two runs |
| getMappedRT | Get mapping of reference RT on experiment run. |
| getMultipeptide | Get multipeptides |
| getMZMLpointers | Get pointers to each mzML file. |
| getNodeIDs | Get node IDs from tree |
| getNodeRun | Create a child run from two parent runs |
| getOswAnalytes | Fetch analytes from OSW file |
| getOswFiles | Get list of peptides and their chromatogram indices. |
| getPeptideQuery | Get peptide scores |
| getPeptideQuery2 | Get peptide scores |
| getPeptideScores | Get scores of peptide |
| getPrecursorByID | Find precursors given their IDs |
| getPrecursors | Get precursors from all feature files |
| getPrecursorsQuery | Get precursor Info |
| getPrecursorsQueryID | Get precursor Info |
| getPrecursorSubset | Prints messages if a certain number of analytes are aligned |
| getQuery | Generate SQL query to fetch information from osw files. |
| getRefRun | Fetch the reference run for each peptide |
| get_ropenms | Get ropenms handle |
| getRSE | Calculates Residual Standard Error of the fit |
| 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 |
| getTransitionsQuery | Get transitions from a SQLite file |
| getTree | Create a phylogenetic tree |
| getXICs | Get XICs of all analytes |
| getXICs4AlignObj | Extract XICs of analytes |
| imputeChromatogram | Fill missing intensities in a chromatogram |
| mapIdxToTime | Establishes mapping from index to time |
| mappedRTfromAlignObj | Map reference run time on the experiment run. |
| mapPrecursorToChromIndices | Merge precursor and transitions mapping with chromatogram... |
| masterXICs_DIAlignR | Master fragment-ion chromatograms from two parents |
| mergeOswAnalytes_ChromHeader | Merge dataframes from OSW and mzML files |
| mergeXIC | Merge two XICs into one |
| multipeptide_DIAlignR | Analytes information from multipeptide. |
| nrDesc | Number of descendants |
| oswFiles_DIAlignR | Analytes information from osw files |
| otherChildXICpp | Get child chromatogram for other precursors using main... |
| paramsDIAlignR | Parameters for the alignment functions |
| perBatch | Aligns an analyte across runs |
| pickNearestFeature | Pick feature closest to reference peak |
| plotAlignedAnalytes | Plot aligned XICs group for a specific peptide.... |
| plotAlignmentPath | Visualize alignment path through similarity matrix |
| plotAnalyteXICs | Plot extracted-ion chromatogram. |
| plotSingleAlignedChrom | Plot an aligned XIC-group. |
| plotXICgroup | Plot Extracted-ion chromatogram group. |
| progAlignRuns | Peptide quantification through progressive alignment |
| progAlignRuns2 | Progressive alignment for few ids |
| readMzMLHeader | Get chromatogram header from a mzML file |
| readSqMassHeader | Get chromatogram header from a sqMass file |
| recalculateIntensity | Calculates area of peaks in peakTable |
| script1 | Extract features and generate pairwise alignments. |
| script2 | Performs alignment using script1 output |
| setAlignmentRank | Set Alignment rank to the aligned feature |
| sgolayCpp | Smooth chromatogram with savitzky-golay filter. |
| sgolayFill | Fill missing values using Savitzky–Golay |
| smoothSingleXIC | Smooth chromatogram signal |
| smoothXICs | Smooth chromatogram signals from a list |
| splineFill | Fill missing values using spline |
| splineFillCpp | Interpolate using spline |
| traverseDown | Traverses down from the root to leaves |
| traverseUp | Traverses up from leaves to the root |
| trfrParentFeature | Transform features to child time-domain |
| trimXICs | Selects a part of chromatograms |
| uncompressVec | Uncompress a Blob object |
| updateFileInfo | Get intersection of runs and fileInfo |
| updateOnalignTargetedRuns | Prints messages if a certain number of analytes are aligned |
| writeTables | Writes the output table post-alignment |
| XIC_QFNNTDIVLLEDFQK_3_DIAlignR | Extracted-ion chromatograms (XICs) of a peptide |
