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

Source: R/MTD.R
setMtdCv.Rd

setMtdCv() sets or updates CV-related metadata fields within an MTD (metadata) section. When CV metadata already exists, the function can either replace it entirely or append new values to the existing ones.

getMtdCv() returns the CV information from an MTD section.

Usage

# S4 method for class 'dfmatrix'
setMtdCv(
  x = matrix(),
  label = character(),
  full_name = character(),
  version = character(),
  uri = character(),
  replace = FALSE
)

getMtdCv(x = matrix())

Arguments

x

A MTD section that stores metadata fields. Can be a two-column character matrix, a two-column data.frame or a MzTabM() object. Defaults to matrix(). If all values are NA, the function returns x unchanged.

label

character describing the labels of the controlled vocabularies/ontologies used in the mzTab-M file (e.g. "MS" for PSI-MS).

full_name

character describing the full names of the controlled vocabularies/ontologies used.

version

character describing the version of the controlled vocabularies/ontologies used. (e.g. "4.1.11")

uri

character containing the URIs of the controlled vocabularies/ ontologies used in the mzTab file. Note: For OBO ontologies, always use an OBO PURL rather than raw repository links to ensure long-term stability (e.g. "https://purl.obolibrary.org/obo/ms.obo"). For other ontology formats, please use the fully qualified PURL pointing to the ontology file.

replace

logical flag controlling how pre-existing CV metadata is handled:

  • FALSE (default): new values are appended to any existing values.

  • TRUE: existing instrument metadata is discarded and replaced entirely by the supplied arguments.

Value

  • For setMtdCv(): the input object x updated to include the new or merged CV metadata fields. If x is empty, the empty x.

  • For getMtdCv(): a named character with the CV information, names being the field names.

Author

Gabriele Tomè

Examples


x <- mtdSkeleton("001", software = "[MS, MS:1001582, xmcs, 4.0.0]")
## Add CV metadata to an existing mzTab object
mtd <- setMtdCv(x, label = "MS",
          full_name = "PSI-MS controlled vocabulary",
          version = "4.1.11",
          uri = "https://purl.obolibrary.org/obo/ms.obo")

## Replace all existing CV metadata
mtd <- setMtdCv(mtd, label = "MS",
          full_name = "PSI-MS controlled vocabulary",
          version = "4.1.11",
          uri = "https://purl.obolibrary.org/obo/ms.obo",
          replace = TRUE)

## Get CV infrmation
getMtdCv(mtd)
#>                              cv[1]-label 
#>                                     "MS" 
#>                          cv[1]-full_name 
#>           "PSI-MS controlled vocabulary" 
#>                            cv[1]-version 
#>                                 "4.1.11" 
#>                                cv[1]-uri 
#> "https://purl.obolibrary.org/obo/ms.obo"