Package: DIAlignR 2.13.0

Shubham Gupta

DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

To obtain unbiased proteome coverage from a biological sample, mass-spectrometer is operated in Data Independent Acquisition (DIA) mode. Alignment of these DIA runs establishes consistency and less missing values in complete data-matrix. This package implements dynamic programming with affine gap penalty based approach for pair-wise alignment of analytes. A hybrid approach of global alignment (through MS2 features) and local alignment (with MS2 chromatograms) is implemented in this tool.

Authors:Shubham Gupta [aut, cre], Hannes Rost [aut], Justin Sing [aut]

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DIAlignR/json (API)
NEWS

# Install 'DIAlignR' in R:

install.packages('DIAlignR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/shubham1637/dialignr/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

XIC_QFNNTDIVLLEDFQK_3_DIAlignR - Extracted-ion chromatograms (XICs) of a peptide
alignObj_DIAlignR - Alignment object of a peptide.
masterXICs_DIAlignR - Master fragment-ion chromatograms from two parents
multipeptide_DIAlignR - Analytes information from multipeptide.
oswFiles_DIAlignR - Analytes information from osw files

On BioConductor:DIAlignR-2.13.0(bioc 3.20)DIAlignR-2.12.0(bioc 3.19)

bioconductor-package

68 exports 0.91 score 71 dependencies

Last updated 2 months agofrom:782a3f0c76

Exports:AffineAlignObj AffineAlignObjLight AffineAlignObjMedium alignChromatogramsCpp AlignObj alignTargetedRuns alignToRoot4 areaIntegrator as.list childXICs constrainSimCpp createMZML createSqMass doAffineAlignmentCpp doAlignmentCpp get_ropenms getAlignedTimes getAlignedTimesCpp getAlignedTimesFast getAlignObj getAlignObjs getBaseGapPenaltyCpp getChildXICpp getChildXICs getChromatogramIndices getChromSimMatCpp getFeatures getGlobalAlignMaskCpp getGlobalAlignment getMultipeptide getMZMLpointers getNativeIDs getPeptideScores getPrecursorByID getPrecursorIndices getPrecursors getRefExpFeatureMap getRefRun getRTdf getRunNames getSeqSimMatCpp getTransitions getXICs getXICs4AlignObj imputeChromatogram mapIdxToTime mstAlignRuns mstScript1 mstScript2 otherChildXICpp paramsDIAlignR plotAlignedAnalytes plotAlignmentPath plotAnalyteXICs plotXICgroup progAlignRuns progComb3 progSplit2 progSplit4 progTree1 recalculateIntensity reduceXICs script1 script2 sgolayCpp smoothXICs splineFillCpp updateFileInfo

Dependencies:ape Biobase BiocGenerics bit bit64 blob cachem cli colorspace cpp11 data.table DBI digest dplyr fansi farver fastmap fastmatch generics ggplot2 glue gtable here igraph isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix memoise mgcv munsell mzR ncdf4 nlme phangorn pillar pkgconfig plogr png pracma ProtGenerics purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppEigen RcppTOML reticulate Rhdf5lib rlang RMSNumpress rprojroot RSQLite scales signal stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr zoo

MS2 chromatograms based alignment of targeted mass-spectrometry runs

Shubham Gupta and Hannes Röst

Rendered fromDIAlignR-vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-04-19
Started: 2018-12-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
An S4 object for class AffineAlignObj	AffineAlignObj AffineAlignObj-class
An S4 object for class AffineAlignObjLight It only contains aligned indices.	AffineAlignObjLight AffineAlignObjLight-class
An S4 object for class AffineAlignObjMedium. It only contains similarity matrix and aligned indices.	AffineAlignObjMedium AffineAlignObjMedium-class
Aligns MS2 extracted-ion chromatograms(XICs) pair.	alignChromatogramsCpp
Alignment object of a peptide.	alignObj_DIAlignR
An S4 object for class AlignObj	AlignObj AlignObj-class
Outputs intensities for each analyte from aligned Targeted-MS runs	alignTargetedRuns
Step 4 for progressive alignment	alignToRoot4
Calculates area between signal-boundaries.	areaIntegrator
Converts instances of class AffineAlignObj into list	as.list,AffineAlignObj-method
Converts instances of class AffineAlignObjLight into list	as.list,AffineAlignObjLight-method
Converts instances of class AffineAlignObjMedium into list	as.list,AffineAlignObjMedium-method
Converts instances of class AlignObj into list	as.list,AlignObj-method
Get child chromatograms from parents	childXICs
Constrain similarity matrix with a mask	constrainSimCpp
Create an mzML file	createMZML
Create an sqMass file	createSqMass
DIAlignR	DIAlignR
Perform affine global and overlap alignment on a similarity matrix	doAffineAlignmentCpp
Perform non-affine global and overlap alignment on a similarity matrix	doAlignmentCpp
Get ropenms handle	get_ropenms
Get aligned Retention times.	getAlignedTimes
Get aligned indices from MS2 extracted-ion chromatograms(XICs) pair.	getAlignedTimesCpp
Get aligned Retention times.	getAlignedTimesFast
Outputs AlignObj from an alignment of two XIC-groups	getAlignObj
AlignObj for analytes between a pair of runs	getAlignObjs
Calculates gap penalty for dynamic programming based alignment.	getBaseGapPenaltyCpp
Get child chromatogram from two parent chromatogram	getChildXICpp
Develop child XICs for precursors	getChildXICs
Get chromatogram indices of precursors.	getChromatogramIndices
Calculates similarity matrix of two fragment-ion chromatogram groups or extracted-ion chromatograms(XICs)	getChromSimMatCpp
Get features from all feature files	getFeatures
Outputs a mask for constraining similarity matrix	getGlobalAlignMaskCpp
Calculates global alignment between RT of two runs	getGlobalAlignment
Get multipeptides	getMultipeptide
Get pointers to each mzML file.	getMZMLpointers
Fetch NativeIDs	getNativeIDs
Get scores of peptide	getPeptideScores
Find precursors given their IDs	getPrecursorByID
Get MS1 chromatogram indices of precursors.	getPrecursorIndices
Get precursors from all feature files	getPrecursors
Alignment Feature Mapping Table	getRefExpFeatureMap
Fetch the reference run for each peptide	getRefRun
Calculates global alignment between RT of two runs	getRTdf
Get names of all runs	getRunNames
Calculates similarity matrix for two sequences	getSeqSimMatCpp
Get transitions from all feature files	getTransitions
Get XICs of all analytes	getXICs
Extract XICs of analytes	getXICs4AlignObj
Fill missing intensities in a chromatogram	imputeChromatogram
Establishes mapping from index to time	mapIdxToTime
Master fragment-ion chromatograms from two parents	masterXICs_DIAlignR
Peptide quantification through MST alignment	mstAlignRuns
Extract features and generate minimum spanning tree.	mstScript1
Performs alignment using mstScript1 output	mstScript2
Analytes information from multipeptide.	multipeptide_DIAlignR
Analytes information from osw files	oswFiles_DIAlignR
Get child chromatogram for other precursors using main precursor alignment	otherChildXICpp
Parameters for the alignment functions	paramsDIAlignR
Plot aligned XICs group for a specific peptide. AlignObjOutput is the output from getAlignObjs fucntion.	plotAlignedAnalytes
Visualize alignment path through similarity matrix	plotAlignmentPath
Plot extracted-ion chromatogram.	plotAnalyteXICs
Plot Extracted-ion chromatogram group.	plotXICgroup
Peptide quantification through progressive alignment	progAlignRuns
Step 3 for progressive alignment	progComb3
Step 2 for progressive alignment	progSplit2
Step 4 for progressive alignment	progSplit4
Step 1 for progressive alignment	progTree1
Calculates area of peaks in peakTable	recalculateIntensity
Subset an XIC file	reduceXICs
Extract features and generate pairwise alignments.	script1
Performs alignment using script1 output	script2
Smooth chromatogram with savitzky-golay filter.	sgolayCpp
Smooth chromatogram signal	smoothSingleXIC
Smooth chromatogram signals from a list	smoothXICs
Interpolate using spline	splineFillCpp
Selects a part of chromatograms	trimXICs
Get intersection of runs and fileInfo	updateFileInfo
Extracted-ion chromatograms (XICs) of a peptide	XIC_QFNNTDIVLLEDFQK_3_DIAlignR