Add or Update a Metadata Field of an mzTab-M MTD section

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

getMtdField() returns the information from an MTD section of the requested field.

Usage

# S4 method for class 'dfmatrix'
setMtdField(
  x = matrix(),
  field = character(),
  value = character(),
  replace = FALSE
)

getMtdField(x = matrix(), field = character())

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.

field

character(1) name of the metadata field to set or update. Must be a valid MTD field name. (e.g. "publication")

value

character value(s) to assign to the field. (e.g. "https://pubs.acs.org/doi/10.1021/acs.analchem.8b04310")

replace

logical flag controlling how pre-existing field metadata is handled. Valid only for indexed fields, unique fields are always replaced.

• 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 setMtdField(): the input object x updated to include the new or merged field metadata. If x is empty, the empty x.

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

Author

Gabriele Tomè

Examples

x <- mtdSkeleton("001", software = "[MS, MS:1001582, xcms, 4.0.0]")
## Add a metadata field to an existing mzTab object
mtd <- setMtdField(x, field = "publication",
          value = "pubmed:21063943|doi:10.1007/978-1-60761-987-1_6")

## Replace all existing values for a metadata field
mtd <- setMtdField(mtd, field = "custom",
          value = "[,,MS operator, Florian]",
          replace = TRUE)

getMtdField(mtd, field = "mzTab-ID")
#> mzTab-ID 
#>    "001"