R API for the mzTab-M Reference Implementation

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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