Skip to contents

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

Source: R/MTD.R
setMtdContact.Rd

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

getMtdContact() returns the contact information from an MTD section.

Usage

# S4 method for class 'dfmatrix'
setMtdContact(
  x = matrix(),
  name = character(),
  affiliation = character(),
  email = character(),
  orcid = character(),
  replace = FALSE
)

getMtdContact(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.

name

character contact’s name.

affiliation

character contact’s affiliation.

email

character contact’s e-mail address.

orcid

character contact’s ORCID identifier.

replace

logical flag controlling how pre-existing contact 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 setMtdContact(): the input object x updated to include the new or merged contact metadata fields. If x is empty, the empty x.

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

Author

Gabriele Tomè

Examples


x <- mtdSkeleton("001", software = "[MS, MS:1001582, xmcs, 4.0.0]")
## Add contact metadata to an existing mzTab object
mtd <- setMtdContact(x, name = "Name Surname",
          affiliation = "PSI-MS",
          email = "name.surname@mail.com", orcid = "0000-0002-1825-0097")

## Replace all existing contact metadata
mtd <- setMtdContact(mtd, name = "Name Surname",
          affiliation = "PSI-MS",
          email = "name.surname@mail.com",
          orcid = "0000-0002-1825-0097",
          replace = TRUE)


getMtdContact(mtd)
#>         contact[1]-name  contact[1]-affiliation        contact[1]-email 
#>          "Name Surname"                "PSI-MS" "name.surname@mail.com" 
#>        contact[1]-orcid 
#>   "0000-0002-1825-0097"