Package: ncGTW 1.27.0

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_1.27.0.tar.gz
ncGTW_1.27.0.zip(r-4.7)ncGTW_1.27.0.zip(r-4.6)ncGTW_1.27.0.zip(r-4.5)
ncGTW_1.27.0.tgz(r-4.6-x86_64)ncGTW_1.27.0.tgz(r-4.6-arm64)ncGTW_1.27.0.tgz(r-4.5-x86_64)ncGTW_1.27.0.tgz(r-4.5-arm64)
ncGTW_1.27.0.tar.gz(r-4.7-arm64)ncGTW_1.27.0.tar.gz(r-4.7-x86_64)ncGTW_1.27.0.tar.gz(r-4.6-arm64)ncGTW_1.27.0.tar.gz(r-4.6-x86_64)
ncGTW_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ncGTW/json (API)

# 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-1.27.0(bioc 3.24)ncGTW-1.26.0(bioc 3.23)

software massspectrometry metabolomics alignment cpp

4.90 score 8 stars 8 scripts 16 exports 135 dependencies

Last updated from:87c9be45d4. Checks:1 ERROR, 4 NOTE, 2 OK, 7 WARNING. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	231
linux-devel-arm64	NOTE	497
linux-devel-x86_64	NOTE	639
source / vignettes	OK	531
linux-release-arm64	NOTE	468
linux-release-x86_64	NOTE	653
macos-release-arm64	WARNING	341
macos-release-x86_64	WARNING	731
macos-oldrel-arm64	WARNING	282
macos-oldrel-x86_64	WARNING	568
windows-devel	WARNING	658
windows-release	WARNING	534
windows-oldrel	WARNING	488
wasm-release	OK	234

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 biocmake BiocManager BiocParallel bslib cachem cli clue cluster codetools cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dir.expiry doParallel dplyr evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options generics 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 mime MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment mzID mzR ncdf4 openssl otel pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch PTMods purrr QFeatures R6 rappdirs RColorBrewer Rcpp reshape2 Rhdf5lib rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite vsn withr xcms xfun XML XVector yaml

ncGTW User Manual

Rendered fromncGTW.Rmdusingknitr::rmarkdown

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