Package: RmzTabM 0.97.19

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. 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]

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DESCRIPTION
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 CRAN:

quarto

4.60 score 3 stars 12 scripts 45 exports 18 dependencies

Last updated from:f0f345d736. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	265
source / vignettes	OK	294
linux-release-x86_64	OK	265
macos-release-arm64	OK	237
macos-oldrel-arm64	OK	198
windows-devel	OK	214
windows-release	OK	213
windows-oldrel	OK	185
wasm-release	OK	137

Exports:assayCols getMtdContact getMtdCv getMtdDatabase getMtdField getMtdInstrument getMtdProtocol isCvParameter makeSummarizedExperimentFromMzTabM msRunCols mtd mtdAssay mtdDefineStudyVariables mtdFields mtdFromSampleData mtdMsRun mtdSample mtdSkeleton mtdSort mtdStudyVariables mtdToSampleData MzTabM 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 Biobase BiocGenerics data.table DelayedArray generics GenomicRanges IRanges lattice Matrix MatrixGenerics matrixStats S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment XVector

The R API for the mzTab-M File Format

Rendered fromrmztabm-api.qmdusingquarto::html

Last update: 2026-07-21
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
msTab-M _ms_run_ metadata fields	mtdMsRun
msTab-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
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 0.97.19

RmzTabM: R API for the mzTab-M Reference Implementation

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