Package: RmzTabM 0.97.16

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]

RmzTabM_0.97.16.tar.gz
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manual.pdf |manual.html✨
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:

Conda:

quarto

3.56 score 3 stars 12 scripts 40 exports 18 dependencies

Last updated from:a11dcbd8aa. Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING269
source / vignettesERROR327
linux-release-x86_64WARNING295
macos-release-arm64WARNING249
macos-oldrel-arm64WARNING217
windows-develWARNING236
windows-releaseWARNING232
windows-oldrelWARNING373
wasm-releaseOK211

Exports:assayColsgetMtdContactgetMtdCvgetMtdDatabasegetMtdFieldgetMtdInstrumentisCvParametermsRunColsmtdmtdAssaymtdDefineStudyVariablesmtdFieldsmtdFromSampleDatamtdMsRunmtdProtocolmtdSamplemtdSkeletonmtdSortmtdStudyVariablesMzTabMparseCvParameterreadMzTabMsampleColssetMtdContactsetMtdCvsetMtdDatabasesetMtdFieldsetMtdInstrumentsmeCreatesmeIdConfidenceMeasuresmeSortsmeSpectraRefValidatorsmfsmfColssmfCreatesmfSortsmlAddStudyVariableColumnssmlCreatesmlSortwriteMzTabM

Dependencies:abindBiobaseBiocGenericsdata.tableDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

Readme and manuals

Help Manual

Help pageTopics
Defining and exporting the mzTab-M metadata tableMTD-export
mzTab-M _assay_ metadata informationmtdAssay
Prepare and format information for the mzTab-M metadata sectionmtdFields
Create the mzTab-M MTD content from a sample data frameassayCols msRunCols mtdFromSampleData sampleCols
msTab-M _ms_run_ metadata fieldsmtdMsRun
mzTab-M _protocol_ metadata informationmtdProtocol
msTab-M _sample_ metadata informationmtdSample
Create a skeleton MTD section with general informationmtdSkeleton
Sort rows in a MTD matrix to match the expected ordermtdSort
mzTab-M _study variables_ metadata informationmtdDefineStudyVariables mtdStudyVariables
mzTab-M data containermtd mtd,MzTabM-method MzTabM MzTabM,dfmatrix-method MzTabM,missing-method MzTabM-class smf smf,MzTabM-method
Export a mzTab-M 2.1 fileMzTabM-export writeMzTabM
Import a mzTab-M 2.1 fileMzTabM-import readMzTabM
Utility functions for CV parametersisCvParameter parseCvParameter
Quantified LC-MS preprocessing result test data from Metabonautse
Add or Update contact Metadata of an mzTab-M MTD sectiongetMtdContact setMtdContact setMtdContact,dfmatrix-method setMtdContact,MzTabM-method
Add or Update Controlled Vocabularies (CV) Metadata of an mzTab-M MTD sectiongetMtdCv setMtdCv setMtdCv,dfmatrix-method setMtdCv,MzTabM-method
Add or Update Database Metadata of an mzTab-M MTD sectiongetMtdDatabase setMtdDatabase setMtdDatabase,dfmatrix-method setMtdDatabase,MzTabM-method
Add or Update a Metadata Field of an mzTab-M MTD sectiongetMtdField setMtdField setMtdField,dfmatrix-method setMtdField,MzTabM-method
Add, update or get instrument metadata of an mzTab-M MTD sectiongetMtdInstrument setMtdInstrument setMtdInstrument,dfmatrix-method setMtdInstrument,MzTabM-method
Creating the mzTab-M Small Molecule (SME) TableSME-export smeCreate smeIdConfidenceMeasure smeSort smeSpectraRefValidator
Create the mzTab-M Small Molecule Feature (SMF) TableSMF-export smfCreate smfSort
Creating the mzTab-M Small Molecule (SML) TableSML-export smlAddStudyVariableColumns smlCreate smlSort
Create a mzTab-M file from a 'SummarizedExperiment' objectMzTabM,SummarizedExperiment-method smf,SummarizedExperiment-method smfCols SummarizedExperiment-mzTab-M