The MzTabM class is a simple container for the mzTab-M data/file content.
Methods for this class allow adding or updating information and validating
its content.
New instances can be created using the MzTabM() function providing the
content for the MTD, SML, SMF and SME sections (through parameters mtd,
sml, smf, and sme, respectively).
Usage
# S4 method for class 'dfmatrix'
MzTabM(
mtd = mtdSkeleton(id = "<replace>", software = "<replace>"),
sml = matrix(ncol = 0, nrow = 0),
smf = matrix(ncol = 0, nrow = 0),
sme = matrix(ncol = 0, nrow = 0)
)
# S4 method for class 'MzTabM'
mtd(object)
# S4 method for class 'MzTabM'
sml(object)
# S4 method for class 'MzTabM'
smf(object)
# S4 method for class 'MzTabM'
sme(object)Arguments
- mtd
Two-column
matrixordata.framewith the MTD content (see MTD-export for details and expected format/content).- sml
matrixordata.framewith the SML content (see SML-export for details and expected format/content).- smf
matrixordata.framewith the SMF content (see SMF-export for details and expected format/content).- sme
matrixordata.framewith the SME content (see SME-export for details and expected format/content).- object
MzTabMobject.
MTD section; adding or getting metadata
Various functions are available to get or set metadata information of a
MzTabM class:
getMtdInstrument()andsetMtdInstrument()for instrument information.getMtdDatabase()andsetMtdDatabase()for database information.getMtdCv()andsetMtdCv()for CV information.getMtdContact()andsetMtdContact()for contact information.getMtdProtocol()andsetMtdProtocol()for protocol information.getMtdField()andsetMtdField()for additional information.
SML section; adding or getting small summary matrix
sml(): returns the SML summary matrix of anMzTabMobject.
SMF section; adding or getting small feature abundance matrix
smf(): returns the SMF feature abundance matrix of anMzTabMobject.
SME section; adding or getting small evidence matrix
sme(): returns the SME evidence matrix of anMzTabMobject.
Examples
## Create a minimal mzTab-M with only MTD content.
m <- MzTabM(mtd = mtdSkeleton(id = "001", software = "[,,RmzTabM,]"))
m
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#> MTD section with 24 rows.
## Add instrument information to the MTD section
m <- setMtdInstrument(m, name = "[MS, MS:1000449, LTQ Orbitrap,]",
source = "[MS, MS:1000073, ESI,]",
analyzer = c(`analyzer[1]` = "[MS, MS:1000291, linear ion trap,]"),
detector = "[MS, MS:1000253, electron multiplier,]")
m
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#> MTD section with 28 rows.
getMtdInstrument(m)
#> instrument[1]-name
#> "[MS, MS:1000449, LTQ Orbitrap,]"
#> instrument[1]-source
#> "[MS, MS:1000073, ESI,]"
#> instrument[1]-analyzer[1]
#> "[MS, MS:1000291, linear ion trap,]"
#> instrument[1]-detector
#> "[MS, MS:1000253, electron multiplier,]"
## Add database metadata to an existing mzTab object
m <- setMtdDatabase(m, name = "[MIRIAM, MIR:00100079, HMDB, ]",
prefix = "hmdb",
version = "3.6",
uri = "http://www.hmdb.ca/")
m
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#> MTD section with 28 rows.
getMtdDatabase(m)
#> database[1] database[1]-prefix
#> "[MIRIAM, MIR:00100079, HMDB, ]" "hmdb"
#> database[1]-version database[1]-uri
#> "3.6" "http://www.hmdb.ca/"
## Add CV metadata to an existing mzTab object
m <- setMtdCv(m, label = "MS",
full_name = "PSI-MS controlled vocabulary",
version = "4.1.11",
uri = "https://purl.obolibrary.org/obo/ms.obo")
m
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#> MTD section with 32 rows.
getMtdCv(m)
#> cv[1]-label
#> "MS"
#> cv[1]-full_name
#> "PSI-MS controlled vocabulary"
#> cv[1]-version
#> "4.1.138"
#> cv[1]-uri
#> "https://www.ebi.ac.uk/ols4/ontologies/ms"
#> cv[2]-label
#> "PRIDE"
#> cv[2]-full_name
#> "PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary"
#> cv[2]-version
#> "16:10:2023 11:38"
#> cv[2]-uri
#> "https://www.ebi.ac.uk/ols/ontologies/pride"
#> cv[3]-label
#> "STATO"
#> cv[3]-full_name
#> "General purpose STATistics Ontology"
#> cv[3]-version
#> "2026-04-20"
#> cv[3]-uri
#> "https://www.ebi.ac.uk/ols4/ontologies/stato"
#> cv[4]-label
#> "MS"
#> cv[4]-full_name
#> "PSI-MS controlled vocabulary"
#> cv[4]-version
#> "4.1.11"
#> cv[4]-uri
#> "https://purl.obolibrary.org/obo/ms.obo"
## Add contact metadata to an existing mzTab object
m <- setMtdContact(m, name = "Name Surname",
affiliation = "PSI-MS",
email = "name.surname@mail.com", orcid = "0000-0002-1825-0097")
m
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#> MTD section with 36 rows.
getMtdContact(m)
#> contact[1]-name contact[1]-affiliation contact[1]-email
#> "Name Surname" "PSI-MS" "name.surname@mail.com"
#> contact[1]-orcid
#> "0000-0002-1825-0097"
## Add protocol metadata to an existing mzTab object
m <- setMtdProtocol(m, name = c("Mass Spectrometry"),
type = c("[CHMO, CHMO:0000470, mass spectrometry, ]"),
description = c("Eluting compounds were detected ..."),
parameters = paste0("[MS, MS:1000008, ionization type, ",
"[MS,MS:1000073, electrospray ionization, ]]"))
m
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#> MTD section with 40 rows.
getMtdProtocol(m)
#> protocol[1]-name
#> "Mass Spectrometry"
#> protocol[1]-type
#> "[CHMO, CHMO:0000470, mass spectrometry, ]"
#> protocol[1]-description
#> "Eluting compounds were detected ..."
#> protocol[1]-parameter[1]
#> "[MS, MS:1000008, ionization type, [MS,MS:1000073, electrospray ionization, ]]"
## Add a metadata field to an existing mzTab object
m <- setMtdField(m, field = "publication",
value = "pubmed:21063943|doi:10.1007/978-1-60761-987-1_6")
m
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#> MTD section with 41 rows.
getMtdField(m, field = "publication")
#> publication[1]
#> "pubmed:21063943|doi:10.1007/978-1-60761-987-1_6"