Package: ncGTW 1.26.0

Chiung-Ting Wu

ncGTW: Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection

The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.

Authors:Chiung-Ting Wu <[email protected]>

ncGTW_1.26.0.tar.gz
ncGTW_1.26.0.zip(r-4.7)ncGTW_1.26.0.zip(r-4.6)ncGTW_1.26.0.zip(r-4.5)
ncGTW_1.26.0.tgz(r-4.6-x86_64)ncGTW_1.26.0.tgz(r-4.6-arm64)ncGTW_1.26.0.tgz(r-4.5-x86_64)ncGTW_1.26.0.tgz(r-4.5-arm64)
ncGTW_1.26.0.tar.gz(r-4.7-arm64)ncGTW_1.26.0.tar.gz(r-4.7-x86_64)ncGTW_1.26.0.tar.gz(r-4.6-arm64)ncGTW_1.26.0.tar.gz(r-4.6-x86_64)
ncGTW_1.26.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ncGTW/json (API)
NEWS

# Install 'ncGTW' in R:
install.packages('ncGTW', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/chiungtingwu/ncgtw/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:ncGTW-1.27.0(bioc 3.24)ncGTW-1.26.0(bioc 3.23)

softwaremassspectrometrymetabolomicsalignmentcpp

4.90 score 8 stars 3 scripts 319 downloads 16 exports 135 dependencies

Last updated from:f18cf12b6f (on RELEASE_3_23). Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR229
linux-devel-arm64NOTE469
linux-devel-x86_64NOTE524
source / vignettesOK500
linux-release-arm64NOTE508
linux-release-x86_64NOTE597
macos-release-arm64NOTE494
macos-release-x86_64NOTE941
macos-oldrel-arm64NOTE400
macos-oldrel-x86_64NOTE937
windows-develNOTE598
windows-releaseNOTE583
windows-oldrelNOTE637
wasm-releaseOK179

Exports:adjustRTalignDatacompCVdownSamplegroupInfoloadProfilemeanCorOlmisalignDetectncGTWalignncGTWpathncGTWpeaksplotGroupprofilesrtncGTWrtRawscanRange

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

ncGTW User Manual

Chiung-Ting Wu

Rendered fromncGTW.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2019-12-30
Started: 2019-06-19

Readme and manuals

Help Manual

Help pageTopics
ncGTW: A package for detecting and aligning the misaligned features in LC-MS datancGTW-package ncGTW
Adjust retention timeadjustRT
ncGTWoutput-accessorsalignData alignData,ncGTWoutput-method
Compare CVcompCV
Edited XCMS fillPeaksChromPar for feature-wise warping functionsfillPeaksChromPar
Edited XCMS getPeaks for feature-wise warping functionsgetPeaksncGTW
ncGTWinput-accessorsdownSample downSample,ncGTWoutput-method groupInfo groupInfo,ncGTWinput-method ncGTWpath ncGTWpath,ncGTWoutput-method profiles profiles,ncGTWinput-method rtRaw rtRaw,ncGTWinput-method scanRange scanRange,ncGTWoutput-method
Load sample profiles for each peak grouploadProfile
Compute average pairwise correlation and overlapping areameanCorOl
Detect misaligned peak groups in xcmsSet object of XCMSmisalignDetect
Run ncGTW alignmentncGTWalign
Class "ncGTWinput"ncGTWinput ncGTWinput-class
Class "ncGTWoutput"ncGTWoutput ncGTWoutput-class
Class "ncGTWparam"ncGTWparam ncGTWparam-class
Class "ncGTWwarp"ncGTWwarp ncGTWwarp-class
Plot profiles for each peak groupplotGroup
ncGTWwarp-accessorsncGTWpeaks ncGTWpeaks,ncGTWwarp-method rtncGTW rtncGTW,ncGTWwarp-method
Examples of xcmsSet for inputs of ncGTWxcmsExamples