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

Source: R/MTD.R
setMtdProtocol.Rd

setMtdProtocol() sets or updates protocol-related metadata fields within an MTD (metadata) section. When protocol metadata already exists, the function can either replace it entirely or append new values to the existing ones. Each protocol is referenced from an assay section (see mtdAssay()).

getMtdProtocol() returns the protocol information from an MTD section.

Usage

# S4 method for class 'dfmatrix'
setMtdProtocol(
  x = matrix(),
  name = character(),
  type = character(),
  description = character(),
  parameters = character(),
  replace = FALSE
)

getMtdProtocol(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 protocol name describing one or more steps of an experimental procedure, such as sample preparation, data acquisition or data processing.

type

character with the protocol type, as defined by the parameter. Can be of length 1 or equal to length(name).

description

optional character with the description of the protocol. Can be of length 1 or equal to length(name).

parameters

optional character with additional parameters of the protocol

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 setMtdProtocol(): the input object x updated to include the new or merged protocol metadata fields. If x is empty, the empty x.

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

Author

Gabriele Tomè

Examples


x <- mtdSkeleton("001", software = "[MS, MS:1001582, xmcs, 4.0.0]")
## Minimal example with protocol.
mtd <- setMtdProtocol(x, 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, ]]"))

## Example with all the fields and replace the previous
mtd <- setMtdProtocol(mtd, name = c("Mass Spectrometry", "extraction"),
            type = c("[CHMO, CHMO:0000470, mass spectrometry, ]",
                     "[MSIO, MSIO:0000141, metabolite extraction,]"),
            description = c("Eluting compounds were detected ...",
                            "Extraction using 80% methanol"),
            parameters = list(c(paste0("[MS, MS:1000008, ionization type, ",
                              "[MS,MS:1000073, electrospray ionization, ]]"),
                              "param1.2"),
                              paste0("[MSIO, MSIO:0000107, quenching, ",
                                 "[MSIO, MSIO:0000109, liquid nitrogen,]]")),
            replace = TRUE)

getMtdProtocol(mtd)
#>                                                                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, ]]" 
#>                                                        protocol[1]-parameter[2] 
#>                                                                      "param1.2" 
#>                                                                protocol[2]-name 
#>                                                                    "extraction" 
#>                                                                protocol[2]-type 
#>                                  "[MSIO, MSIO:0000141, metabolite extraction,]" 
#>                                                         protocol[2]-description 
#>                                                 "Extraction using 80% methanol" 
#>                                                        protocol[2]-parameter[1] 
#>       "[MSIO, MSIO:0000107, quenching, [MSIO, MSIO:0000109, liquid nitrogen,]]"