Package: ncGTW 1.21.0

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_1.21.0.tar.gz
ncGTW_1.21.0.zip(r-4.5)ncGTW_1.21.0.zip(r-4.4)ncGTW_1.21.0.zip(r-4.3)
ncGTW_1.21.0.tgz(r-4.4-x86_64)ncGTW_1.21.0.tgz(r-4.4-arm64)ncGTW_1.21.0.tgz(r-4.3-x86_64)ncGTW_1.21.0.tgz(r-4.3-arm64)
ncGTW_1.21.0.tar.gz(r-4.5-noble)ncGTW_1.21.0.tar.gz(r-4.4-noble)
ncGTW_1.21.0.tgz(r-4.4-emscripten)ncGTW_1.21.0.tgz(r-4.3-emscripten)
ncGTW.pdf |ncGTW.html✨
ncGTW/json (API)
NEWS

# Install 'ncGTW' in R:

install.packages('ncGTW', repos = c('https://bioc.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:

xcmsExamples - Examples of xcmsSet for inputs of ncGTW

On BioConductor:ncGTW-1.21.0(bioc 3.21)ncGTW-1.20.0(bioc 3.20)

software massspectrometry metabolomics alignment

4.85 score 7 stars 3 scripts 362 downloads 16 exports 137 dependencies

Last updated 25 days agofrom:5de9a8ff5e. Checks:OK: 1 NOTE: 6 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	NOTE	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-win-x86_64	NOTE	Oct 31 2024
R-4.4-mac-x86_64	NOTE	Oct 31 2024
R-4.4-mac-aarch64	WARNING	Oct 31 2024
R-4.3-win-x86_64	NOTE	Oct 31 2024
R-4.3-mac-x86_64	NOTE	Oct 31 2024
R-4.3-mac-aarch64	WARNING	Oct 31 2024

Exports:adjustRT alignData compCV downSample groupInfo loadProfile meanCorOl misalignDetect ncGTWalign ncGTWpath ncGTWpeaks plotGroup profiles rtncGTW rtRaw scanRange

Dependencies:abind affy affyio AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel bslib cachem cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr hms htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MALDIquant MASS MassSpecWavelet Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mgcv mime MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment munsell mzID mzR ncdf4 nlme openssl pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 Rhdf5lib rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite vsn withr xcms xfun XML XVector yaml zlibbioc

ncGTW User Manual

Chiung-Ting Wu

Rendered fromncGTW.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ncGTW: A package for detecting and aligning the misaligned features in LC-MS data	ncGTW-package ncGTW
Adjust retention time	adjustRT
ncGTWoutput-accessors	alignData alignData,ncGTWoutput-method
Compare CV	compCV
Edited XCMS fillPeaksChromPar for feature-wise warping functions	fillPeaksChromPar
Edited XCMS getPeaks for feature-wise warping functions	getPeaksncGTW
ncGTWinput-accessors	downSample 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 group	loadProfile
Compute average pairwise correlation and overlapping area	meanCorOl
Detect misaligned peak groups in xcmsSet object of XCMS	misalignDetect
Run ncGTW alignment	ncGTWalign
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 group	plotGroup
ncGTWwarp-accessors	ncGTWpeaks ncGTWpeaks,ncGTWwarp-method rtncGTW rtncGTW,ncGTWwarp-method
Examples of xcmsSet for inputs of ncGTW	xcmsExamples