This package is considered a duplicate. The official version of this package is found at:https://bioc.r-universe.dev/RmzTabM

Package: RmzTabM 0.99.3

Johannes Rainer

RmzTabM: R API for the mzTab-M Reference Implementation

The RmzTabM package provides functions to read and write files in the HUPO-PSI mzTab-M file format for reporting of results from metabolomics and lipidomics experiments. This package represents the reference implementation for mzTab-M import/export for R. Core, low level functions allow to format and parse the individual sections of the mzTab-M format. These functions are designed to be re-used by other packages implementing import/export of results in mzTab-M.

Authors:Nils Hoffmann [ctb], Steffen Neumann [ctb], Johannes Rainer [aut, cre], Philippine Louail [aut], Gabriele Tomè [aut]

RmzTabM_0.99.3.tar.gz
RmzTabM_0.99.3.zip(r-4.7-any)RmzTabM_0.99.3.zip(r-4.6-any)RmzTabM_0.97.20.zip(r-4.5-any)
RmzTabM_0.99.3.tgz(r-4.6-any)RmzTabM_0.97.20.tgz(r-4.5-any)
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RmzTabM_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RmzTabM/json (API)

# Install 'RmzTabM' in R:

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

Bug tracker:https://github.com/rformassspectrometry/rmztabm/issues

Datasets:

se - Quantified LC-MS preprocessing result test data from Metabonaut

On BioConductor:RmzTabM-0.99.2(bioc 3.24)

infrastructure massspectrometry metabolomics proteomics quarto

5.91 score 3 stars 16 scripts 47 exports 54 dependencies

Last updated from:74385bddd7. Checks:7 OK, 2 FAIL. Indexed: no.

Target	Result	Time
linux-devel	OK	293
source / vignettes	OK	344
linux-release	OK	273
macos-release	OK	318
macos-oldrel	FAIL	113
windows-devel	OK	288
windows-release	OK	242
windows-oldrel	FAIL	118
wasm-release	OK	159

Exports:assayCols getMtdContact getMtdCv getMtdDatabase getMtdField getMtdInstrument getMtdProtocol isCvParameter makeSummarizedExperimentFromMzTabM msRunCols mtd mtdAssay mtdDefineStudyVariables mtdFields mtdFromSampleData mtdMsRun mtdSample mtdSkeleton mtdSort mtdStudyVariables mtdToSampleData MzTabM mzTabMValidator mzTabMValidator_download parseCvParameter readMzTabM sampleCols setMtdContact setMtdCv setMtdDatabase setMtdField setMtdInstrument setMtdProtocol sme smeCreate smeIdConfidenceMeasure smeSort smeSpectraRefValidator smf smfCols smfCreate smfSort sml smlAddStudyVariableColumns smlCreate smlSort writeMzTabM

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli cpp11 curl data.table DBI dbplyr DelayedArray dplyr fastmap filelock generics GenomicRanges glue httr2 IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig purrr R6 rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector

The R API for the mzTab-M File Format

Rendered fromrmztabm-api.qmdusingquarto::html

Last update: 2026-10-14
Started: 2025-12-09

Help page	Topics
Defining and exporting the mzTab-M metadata table	MTD-export
mzTab-M _assay_ metadata information	mtdAssay
Prepare and format information for the mzTab-M metadata section	mtdFields
Create the mzTab-M MTD content from a sample data frame	assayCols msRunCols mtdFromSampleData sampleCols
mzTab-M _ms_run_ metadata fields	mtdMsRun
mzTab-M _sample_ metadata information	mtdSample
Create a skeleton MTD section with general information	mtdSkeleton
Sort rows in a MTD matrix to match the expected order	mtdSort
mzTab-M _study variables_ metadata information	mtdDefineStudyVariables mtdStudyVariables
Reconstruct a sample data frame from mzTab-M MTD content	mtdToSampleData
mzTab-M data container	mtd mtd,MzTabM-method MzTabM MzTabM,dfmatrix-method MzTabM,missing-method MzTabM-class sme sme,MzTabM-method smf smf,MzTabM-method sml sml,MzTabM-method
Export a mzTab-M 2.1 file	MzTabM-export writeMzTabM
Import a mzTab-M 2.1 file	MzTabM-import readMzTabM
Validate an mzTab-M file using the official jmztabm-validator	mzTabMValidator
Download the jmztabm-validator binary	mzTabMValidator_download
Utility functions for CV parameters	isCvParameter parseCvParameter
Quantified LC-MS preprocessing result test data from Metabonaut	se
Add or Update contact Metadata of an mzTab-M MTD section	getMtdContact setMtdContact setMtdContact,dfmatrix-method setMtdContact,MzTabM-method
Add or Update Controlled Vocabularies (CV) Metadata of an mzTab-M MTD section	getMtdCv setMtdCv setMtdCv,dfmatrix-method setMtdCv,MzTabM-method
Add or Update Database Metadata of an mzTab-M MTD section	getMtdDatabase setMtdDatabase setMtdDatabase,dfmatrix-method setMtdDatabase,MzTabM-method
Add or Update a Metadata Field of an mzTab-M MTD section	getMtdField setMtdField setMtdField,dfmatrix-method setMtdField,MzTabM-method
Add, update or get instrument metadata of an mzTab-M MTD section	getMtdInstrument setMtdInstrument setMtdInstrument,dfmatrix-method setMtdInstrument,MzTabM-method
Add or Update protocol Metadata of an mzTab-M MTD section	getMtdProtocol setMtdProtocol setMtdProtocol,dfmatrix-method setMtdProtocol,MzTabM-method
Creating the mzTab-M Small Molecule (SME) Table	SME-export smeCreate smeIdConfidenceMeasure smeSort smeSpectraRefValidator
Create the mzTab-M Small Molecule Feature (SMF) Table	SMF-export smfCreate smfSort
Creating the mzTab-M Small Molecule (SML) Table	SML-export smlAddStudyVariableColumns smlCreate smlSort
Create a mzTab-M file from a 'SummarizedExperiment' object	makeSummarizedExperimentFromMzTabM MzTabM,SummarizedExperiment-method smf,SummarizedExperiment-method smfCols SummarizedExperiment-mzTab-M

Package: RmzTabM 0.99.3

RmzTabM: R API for the mzTab-M Reference Implementation

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