Man pages for DIAlignR
Dynamic Programming Based Alignment of MS2 Chromatograms

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.
AlignObj-classAn S4 object for class AlignObj
alignTargetedRunsOutputs intensities for each analyte from aligned Targeted-MS...
analytesFromFeaturesOutputs analytes below FDR
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
calculateIntensityCalculates area of a peak in XIC group
chromatogramIdAsIntegerCoerce chromatogram ids as integer
constrainSimCppConstrain similarity matrix with a mask
doAffineAlignmentCppPerform affine global and overlap alignment on a similarity...
doAlignmentCppPerform non-affine global and overlap alignment on a...
extractXIC_groupExtract XICs of chromIndices
fetchAnalytesInfoFetch features of analytes
fetchFeaturesFromRunGet features from a feature file.
fetchPrecursorsInfoGet precursors 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 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...
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.
getMultipeptideGet multipeptides
getMZMLpointersGet pointers to each mzML file.
getOswAnalytesFetch analytes from OSW file
getOswFilesGet list of peptides and their chromatogram indices.
getPrecursorByIDFind precursors given their IDs
getPrecursorsGet precursors from all feature files
getPrecursorsQueryGet precursor Info
getPrecursorsQueryIDGet precursor Info
getQueryGenerate SQL query to fetch information from osw files.
getRefRunFetch the reference run for each precursor
getRSECalculates Residual Standard Error of the fit
getRunNamesGet names of all runs
getSeqSimMatCppCalculates similarity matrix for two sequences
getXICsGet XICs of all analytes
getXICs4AlignObjExtract XICs of analytes
mapIdxToTimeEstablishes mapping from index to time
mappedRTfromAlignObjMap reference run time on the experiment run.
mapPrecursorToChromIndicesMerge precursor and transitions mapping with chromatogram...
mergeOswAnalytes_ChromHeaderMerge dataframes from OSW and mzML files
multipeptide_DIAlignRAnalytes information from multipeptide.
oswFiles_DIAlignRAnalytes information from osw files
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.
readChromatogramHeaderGet chromatogram header from a mzML file
setAlignmentRankSet Alignment rank to the aligned feature
smoothSingleXICSmooth chromatogram signal
smoothXICsSmooth chromatogram signals from a list
trimXICsSelects a part of chromatograms
updateFileInfoGet intersection of runs and fileInfo
writeTablesWrites the output table post-alignment
XIC_QFNNTDIVLLEDFQK_3_DIAlignRExtracted-ion chromatograms (XICs) of a peptide
DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.