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

Source: R/MTD.R
setMtdDatabase.Rd

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

getMtdDatabase() returns the database information from an MTD section.

Usage

# S4 method for class 'dfmatrix'
setMtdDatabase(
  x = matrix(),
  name = character(),
  prefix = character(),
  version = character(),
  uri = character(),
  replace = FALSE
)

getMtdDatabase(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 with the description of databases used. For cases, where a known database has not been used for identification. (e.g., "[MIRIAM, MIR:00100079, HMDB, ]").

prefix

character with the prefix used in the “identifier” column of data tables. (e.g., "hmdb").

version

character with the database version is mandatory where identification has been performed. This may be a formal version number ("1.4.1"), a date of access ("2016-10-27") (ISO-8601 format) or ("Unknown") if there is no suitable version that can be annotated.

uri

character with the URI to the database.

replace

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

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

Author

Gabriele Tomè

Examples


x <- mtdSkeleton("001", software = "[MS, MS:1001582, xmcs, 4.0.0]")
## Add database metadata to an existing mzTab object
mtd <- setMtdDatabase(x, name = "[MIRIAM, MIR:00100079, HMDB, ]",
          prefix = "hmdb",
          version = "3.6",
          uri = "http://www.hmdb.ca/")

## Replace all existing database metadata
mtd <- setMtdDatabase(mtd, name = "[MIRIAM, MIR:00100079, HMDB, ]",
          prefix = "hmdb",
          version = "3.6",
          uri = "http://www.hmdb.ca/",
          replace = TRUE)

## Get the database metadata
getMtdDatabase(mtd)
#>                      database[1]               database[1]-prefix 
#> "[MIRIAM, MIR:00100079, HMDB, ]"                           "hmdb" 
#>              database[1]-version                  database[1]-uri 
#>                            "3.6"            "http://www.hmdb.ca/"