Package: metaMS 1.43.0

Yann Guitton

metaMS: MS-based metabolomics annotation pipeline

MS-based metabolomics data processing and compound annotation pipeline.

Authors:Ron Wehrens [aut], Pietro Franceschi [aut], Nir Shahaf [ctb], Matthias Scholz [ctb], Georg Weingart [ctb], Elisabete Carvalho [ctb], Yann Guitton [ctb, cre], Julien Saint-Vanne [ctb]

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metaMS.pdf |metaMS.html✨
metaMS/json (API)
NEWS

# Install 'metaMS' in R:

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

Bug tracker:https://github.com/yguitton/metams/issues

Datasets:

DB - Information on three chemical standards measured in GC-MS
GCresults - Results of metaMS for a small GC-MS data set
LCDBtest - Sample DB for LC-MS annotation
LCresults - Result metaMS for a small LC-MS data set
Orbitrap.RP - Example settings for 'metaMS'
Synapt.NP - Example settings for 'metaMS'
Synapt.RP - Example settings for 'metaMS'
TSQXLS.GC - Example settings for 'metaMS'
errf - Mass error surface for Waters Synapt Q-TOF spectrometers
exptable - Sample table for the generation of a database of standards
smallDB - Information on three chemical standards measured in GC-MS
stdInfo - Information on three chemical standards measured in GC-MS

On BioConductor:metaMS-1.43.0(bioc 3.21)metaMS-1.42.0(bioc 3.20)

immunooncology massspectrometry metabolomics

7.47 score 15 stars 14 scripts 417 downloads 13 mentions 33 exports 153 dependencies

Last updated 2 months agofrom:5510242655. Checks:OK: 3 NOTE: 1 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	WARNING	Nov 19 2024
R-4.5-linux	NOTE	Dec 19 2024
R-4.4-win	WARNING	Nov 19 2024
R-4.4-mac	OK	Dec 19 2024
R-4.3-win	WARNING	Nov 19 2024
R-4.3-mac	OK	Dec 19 2024

Exports:addRI alignmentLC AnnotateFeature AnnotateTable construct.msp constructExpPseudoSpectra createSTDdbGC createSTDdbLC filter.msp generateStdDBGC generateStdDBLC getAnnotationLC getAnnotationMat getFeatureInfo getPeakTable matchExpSpec matchSamples2DB matchSamples2Samples metaMSsettings metaSetting metaSetting<-peakDetection plotPseudoSpectrum processStandards read.msp readStdInfo runCAMERA runGC runLC show to.msp treat.DB write.msp

Dependencies:abind affy affyio AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel bslib cachem CAMERA checkmate cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray DEoptimR digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue graph gridExtra gtable highr Hmisc hms htmlTable 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 nnet openssl pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch purrr QFeatures R6 rappdirs RBGL RColorBrewer Rcpp reshape2 Rhdf5lib rlang rmarkdown robustbase rpart rstudioapi S4Arrays S4Vectors sass scales snow SparseArray Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridis viridisLite vsn withr xcms xfun XML XVector yaml zlibbioc

runGC

Rendered fromrunGC.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2014-03-31
Started: 2014-03-31

runLC

Rendered fromrunLC.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2014-08-01
Started: 2014-03-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analysis pipeline for MS-based metabolomics data	metaMS-package metaMS
Add retention index information to an msp object	addRI
LC alignment	alignmentLC
Annotate a Peaktable	AnnotateFeature AnnotateTable
Conversion of a list of annotation results into a table	annotations2tab makeAnnotation
Create a list of all pseudospectra found in a GC-MS experiment of several samples.	constructExpPseudoSpectra
Create an in-house database for GC-MS annotation	createSTDdbGC generateStdDBGC
Create an in-house database for LC-MS annotation	createSTDdbLC generateStdDBLC
Mass error surface for Waters Synapt Q-TOF spectrometers	errf
Sample table for the generation of a database of standards (LCMS)	exptable
Example settings for 'metaMS'	FEMsettings Orbitrap.RP Synapt.NP Synapt.RP TSQXLS.GC
Results of metaMS for a small GC-MS data set	GCresults
Get LC annotation	getAnnotationLC
Obtain relative quantitative annotation results for GC-MS	getAnnotationMat relInt
Construct an object containing all meta-information of the annotated pseudospectra (GC-MS).	getFeatureInfo
Extract a peak table from an xcms or CAMERA object	getPeakTable
Sample DB for LC-MS annotation	LCDBtest
Result metaMS for a small LC-MS data set	LCresults LCxset
Match GC-MS spectra to an external reference DB	match2ExtDB
Match a GC-MS pseudospectrum to a database with a weighted crossproduct criterion.	matchExpSpec
Match pseudospectra from several samples to an in-house DB (GC-MS)	matchSamples2DB
Compare pseudospectra across samples (GC-MS)	match.unannot.patterns matchSamples2Samples
Class '"metaMSsettings"'	metaMSsettings metaMSsettings-class show,metaMSsettings-method
Get or set values in metaMSsettings objects	metaSetting metaSetting,metaMSsettings-method metaSetting<- metaSetting<-,metaMSsettings-method
Functions to handle msp-type objects (GC-MS)	construct.msp filter.msp msp read.msp SearchNIST to.msp write.msp xset2msp
Wrapper for XCMS peak detection, to be used for both GC-MS and LC-MS data.	peakDetection
Plot a pseudospectrum.	plotPseudoSpectrum
Functions for metaMS-formatted text output	printInfo printString printWarning
Process input files containing raw data for pure standards.	processStandards
Read information of GC injections of standards from a csv file	readStdInfo
Remove double m/z entries in a pseudospectrum	removeDoubleMasses
The CAMERA element in the metaMS pipeline	runCAMERA
Wrapper for processing of GC-MS data files	runGC
Wrapper for processing of LC-MS data files	runLC
Information on three chemical standards measured in GC-MS (liquid injection)	DB smallDB stdInfo threeStdsDB threeStdsInfo threeStdsNIST
Scaling of pseudospectra in an msp object	treat.DB