# R API for the mzTab-M Reference Implementation

## Documentation for package ‘RmzTabM’ version 0.99.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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