Package index

All functions

MTD-export

Defining and exporting the mzTab-M metadata table

writeMzTabM()

Export a mzTab-M 2.1 file

readMzTabM()

Import a mzTab-M 2.1 file

MzTabM(<dfmatrix>) mtd(<MzTabM>) sml(<MzTabM>) smf(<MzTabM>) sme(<MzTabM>)

mzTab-M data container

smeCreate() smeSort() smeIdConfidenceMeasure() smeSpectraRefValidator()

Creating the mzTab-M Small Molecule (SME) Table

smfCreate() smfSort()

Create the mzTab-M Small Molecule Feature (SMF) Table

smlCreate() smlSort() smlAddStudyVariableColumns()

Creating the mzTab-M Small Molecule (SML) Table

MzTabM(<SummarizedExperiment>) smf(<SummarizedExperiment>) makeSummarizedExperimentFromMzTabM() smfCols()

Create a mzTab-M file from a SummarizedExperiment object

mtdAssay()

mzTab-M assay metadata information

mtdFields()

Prepare and format information for the mzTab-M metadata section

mtdFromSampleData() sampleCols() msRunCols() assayCols()

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() mtdDefineStudyVariables()

mzTab-M study variables metadata information

mtdToSampleData()

Reconstruct a sample data frame from mzTab-M MTD content

mzTabMValidator()

Validate an mzTab-M file using the official jmztabm-validator

mzTabMValidator_download()

Download the jmztabm-validator binary

parseCvParameter() isCvParameter()

Utility functions for CV parameters

se

Quantified LC-MS preprocessing result test data from Metabonaut

setMtdContact(<dfmatrix>) getMtdContact()

Add or Update contact Metadata of an mzTab-M MTD section

setMtdCv(<dfmatrix>) getMtdCv()

Add or Update Controlled Vocabularies (CV) Metadata of an mzTab-M MTD section

setMtdDatabase(<dfmatrix>) getMtdDatabase()

Add or Update Database Metadata of an mzTab-M MTD section

setMtdField(<dfmatrix>) getMtdField()

Add or Update a Metadata Field of an mzTab-M MTD section

setMtdInstrument(<dfmatrix>) getMtdInstrument()

Add, update or get instrument metadata of an mzTab-M MTD section

setMtdProtocol(<dfmatrix>) getMtdProtocol()

Add or Update protocol Metadata of an mzTab-M MTD section