Man pages for shubham1637/DIAlign
Dynamic Programming Based Alignment of MS2 Chromatograms

addFlankToLeftAdd signal to the left of XIC
addFlankToRightAdd signal to the right of XIC
addXICAdd XIC to pyopenms experiment
AffineAlignObj-classAn S4 object for class AffineAlignObj
AffineAlignObjLight-classAn S4 object for class AffineAlignObjLight It only contains...
AffineAlignObjMedium-classAn S4 object for class AffineAlignObjMedium. It only contains...
alignChromatogramsCppAligns MS2 extracted-ion chromatograms(XICs) pair.
alignedXICCreate an aligned chromatogram
alignmentStatsPrints alignment summary
AlignObj-classAn S4 object for class AlignObj
alignObj_DIAlignRAlignment object of a peptide.
alignTargetedRunsOutputs intensities for each analyte from aligned Targeted-MS...
alignToMasterAlign descendants to master
alignToRefAligns an analyte from an experiment to the reference run
alignToRefMSTAligns an analyte for an edge of MST
alignToRoot4Step 4 for progressive alignment
analytesFromFeaturesOutputs analytes below FDR
approxFillFill missing values using linear interpolation
areaIntegratorCalculates area between signal-boundaries.
as.list-AffineAlignObjLight-methodConverts instances of class AffineAlignObjLight into list
as.list-AffineAlignObjMedium-methodConverts instances of class AffineAlignObjMedium into list
as.list-AffineAlignObj-methodConverts instances of class AffineAlignObj into list
as.list-AlignObj-methodConverts instances of class AlignObj into list
blobXICsFormat XICs to blob
calculateIntensityCalculates area of a peak in XIC group
checkOverlapOverlap of two time ranges
checkParamsChecks all the alignment parameters
childXICGet a child chromatogram from parents
childXICsGet child chromatograms from parents
chromatogramIdAsIntegerCoerce chromatogram ids as integer
constrainSimCppConstrain similarity matrix with a mask
createMZMLCreate an mzML file
createSqMassCreate an sqMass file
DIAlignRDIAlignR
dialignrLoessModified loess for condition handling
doAffineAlignmentCppPerform affine global and overlap alignment on a similarity...
doAlignmentCppPerform non-affine global and overlap alignment on a...
extractXIC_groupExtract XICs of chromIndices
extractXIC_group2Extract XICs of chromIndices
fetchAnalytesInfoFetch features of analytes
fetchFeaturesFromRunGet features from a feature file.
fetchPeptidesInfoGet scores of all peptides
fetchPeptidesInfo2Get scores of all peptides
fetchPrecursorsInfoGet precursors from a feature file
fetchTransitionsFromRunGet transitions from a feature file
filenamesFromMZMLGet mzML filenames from the directory.
filenamesFromOSWGet mzML filenames from osw RUN table.
getAlignedFigsPlot aligned XICs group for a specific peptide.
getAlignedIndicesGet aligned indices.
getAlignedTimesGet aligned Retention times.
getAlignedTimesCppGet aligned indices from MS2 extracted-ion...
getAlignedTimesFastGet aligned Retention times.
getAlignObjOutputs AlignObj from an alignment of two XIC-groups
getAlignObjsAlignObj for analytes between a pair of runs
getAnalytesQueryGenerate SQL query to fetch limited information from osw...
getBaseGapPenaltyCppCalculates gap penalty for dynamic programming based...
getChildFeatureTransform features to child time-domain
getChildXICppGet child chromatogram from two parent chromatogram
getChildXICsDevelop child XICs for precursors
getChromatogramIndicesGet chromatogram indices of precursors.
getChromSimMatCppCalculates similarity matrix of two fragment-ion chromatogram...
getFeaturesGet features from all feature files
getFeaturesQueryGet features from a SQLite file
getGlobalAlignMaskCppOutputs a mask for constraining similarity matrix
getGlobalAlignmentCalculates global alignment between RT of two runs
getGlobalFitsCalculates all global alignment needed in refRun
getLinearfitCalculates linear fit between RT of two runs
getLOESSfitCalculates LOESS fit between RT of two runs
getMappedRTGet mapping of reference RT on experiment run.
getMSTCreate a MST from distance matrix
getMultipeptideGet multipeptides
getMZMLpointersGet pointers to each mzML file.
getNativeIDsFetch NativeIDs
getNodeIDsGet node IDs from tree
getNodeRunCreate a child run from two parent runs
getOswAnalytesFetch analytes from OSW file
getOswFilesGet list of peptides and their chromatogram indices.
getPeptideQueryGet peptide scores
getPeptideQuery2Get peptide scores
getPeptideScoresGet scores of peptide
getPrecursorByIDFind precursors given their IDs
getPrecursorIndicesGet MS1 chromatogram indices of precursors.
getPrecursorsGet precursors from all feature files
getPrecursorsQueryGet precursor Info
getPrecursorsQueryIDGet precursor Info
getPrecursorSubsetPrints messages if a certain number of analytes are aligned
getQueryGenerate SQL query to fetch information from osw files.
getRefExpFeatureMapAlignment Feature Mapping Table
getRefRunFetch the reference run for each peptide
get_ropenmsGet ropenms handle
getRSECalculates Residual Standard Error of the fit
getRTdfCalculates global alignment between RT of two runs
getRunNamesGet names of all runs
getSeqSimMatCppCalculates similarity matrix for two sequences
getTransitionsGet transitions from all feature files
getTransitionsQueryGet transitions from a SQLite file
getTreeCreate a phylogenetic tree
getXICsGet XICs of all analytes
getXICs4AlignObjExtract XICs of analytes
imputeChromatogramFill missing intensities in a chromatogram
ipfReassignFDRRe-Assign FDR Aligned Peaks
mapIdxToTimeEstablishes mapping from index to time
mappedRTfromAlignObjMap reference run time on the experiment run.
mapPrecursorToChromIndicesMerge precursor and transitions mapping with chromatogram...
masterXICs_DIAlignRMaster fragment-ion chromatograms from two parents
mergeOswAnalytes_ChromHeaderMerge dataframes from OSW and mzML files
mergeXICMerge two XICs into one
mstAlignRunsPeptide quantification through MST alignment
MSTperBatchAligns an analyte for a batch of peptides
mstScript1Extract features and generate minimum spanning tree.
mstScript2Performs alignment using mstScript1 output
multipeptide_DIAlignRAnalytes information from multipeptide.
nrDescNumber of descendants
oswFiles_DIAlignRAnalytes information from osw files
otherChildXICppGet child chromatogram for other precursors using main...
paramsDIAlignRParameters for the alignment functions
perBatchAligns an analyte across runs
pickNearestFeaturePick feature closest to reference peak
plotAlignedAnalytesPlot aligned XICs group for a specific peptide....
plotAlignmentPathVisualize alignment path through similarity matrix
plotAnalyteXICsPlot extracted-ion chromatogram.
plotSingleAlignedChromPlot an aligned XIC-group.
plotXICgroupPlot Extracted-ion chromatogram group.
populateReferenceExperimentFeatureAlignmentMapPopulate Alignment Feature Mapping Table
progAlignRunsPeptide quantification through progressive alignment
progComb3Step 3 for progressive alignment
progSplit2Step 2 for progressive alignment
progSplit4Step 4 for progressive alignment
progTree1Step 1 for progressive alignment
readMzMLHeaderGet chromatogram header from a mzML file
readSqMassHeaderGet chromatogram header from a sqMass file
recalculateIntensityCalculates area of peaks in peakTable
reduceXICsSubset an XIC file
script1Extract features and generate pairwise alignments.
script2Performs alignment using script1 output
setAlignmentRankSet Alignment rank to the aligned feature
sgolayCppSmooth chromatogram with savitzky-golay filter.
sgolayFillFill missing values using Savitzky–Golay
smoothSingleXICSmooth chromatogram signal
smoothXICsSmooth chromatogram signals from a list
splineFillFill missing values using spline
splineFillCppInterpolate using spline
traverseDownTraverses down from the root to leaves
traverseMSTReorder MST
traverseUpTraverses up from leaves to the root
trfrParentFeatureTransform features to child time-domain
trimXICsSelects a part of chromatograms
uncompressVecUncompress a Blob object
updateFileInfoGet intersection of runs and fileInfo
updateOnalignTargetedRunsPrints messages if a certain number of analytes are aligned
writeOutFeatureAlignmentMapWrite out alignment map to disk
writeTablesWrites the output table post-alignment
XIC_QFNNTDIVLLEDFQK_3_DIAlignRExtracted-ion chromatograms (XICs) of a peptide
shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.