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Add, update or get instrument metadata of an mzTab-M MTD section

Source: R/MTD.R
setMtdInstrument.Rd

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

getMtdInstrument() returns the instrument information from an MTD section.

Usage

# S4 method for class 'dfmatrix'
setMtdInstrument(
  x = matrix(),
  name = character(),
  source = character(),
  analyzer = character(),
  detector = character(),
  replace = FALSE
)

getMtdInstrument(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 name of the instrument used in the experiment. (e.g., "[MS, MS:1000449, LTQ Orbitrap,]").

source

character with the instrument’s source used in the experiment. (e.g., "[MS, MS:1000073, ESI,]").

analyzer

character with the instrument’s analyzer type(s) used in the experiment. Must be provided in the form c("analyzer[1]" = "[MS, MS:1000291, linear ion trap,]") for a single analyzer, or c("analyzer[1]" = "<analyzer 1>", "analyzer[2] = ...") for multiple analyzers.

detector

character with the instrument’s detector type used in the experiment. (e.g., "[MS, MS:1000253, electron multiplier,]").

replace

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

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

Author

Gabriele Tomè

Examples


x <- mtdSkeleton("001", software = "[MS, MS:1001582, xmcs, 4.0.0]")
## Add instrument metadata to an existing mzTab object
mtd <- setMtdInstrument(x, 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,]")

## Replace all existing instrument metadata
mtd <- setMtdInstrument(mtd, 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,]",
          replace = TRUE)

x <- mtdSkeleton("001", software = "[MS, MS:1001582, xcms, 4.0.0]")
mtd <- setMtdInstrument(x, 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,]")

getMtdInstrument(mtd)
#>                       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,]"