Utility functions for CV parameters

mzTab-M makes use of controlled vocabulary (CV) parameters. These parameters are expected to be provided in the format "[CV label, accession, name, value]". In addition, also user parameters where only the name and value are provided are supported, but it is recommendet to use full CV parameters where possible.

parseCvParameter() allows to extract individual fields from a CV parameter.

isCvParameter() tests whether a string is in the expected (CV parameter) format.

Usage

parseCvParameter(x, element = 2L)

isCvParameter(x)

Arguments

x

character with the CV parameter(s) to parse or test.

element

integer(1) defining which element to extract: 1 for the CV label, 2 for the CV term (accession), 3 for the name and 4 for the value element.

Value

character of length(x) with the parsed CV parameter elements or NA_character_ if not present.

Note

While mzTab supports "," in the name and value field (in which case the respective field must be placed between "), this is currently not supported. Thus, CV label and term (accession) are expected to be correctly extracted, the name and value field might not if "," are present in them.

Author

Johannes Rainer

Examples

## Extract CV term
x <- c("[MS, MS:1002962, mean, ]", "[MS, MS:1002883, median, ]")
parseCvParameter(x, 1)
#> [1] "MS" "MS"

parseCvParameter(x)
#> [1] "MS:1002962" "MS:1002883"

parseCvParameter(x, 3)
#> [1] "mean"   "median"

parseCvParameter(x, 4)
#> [1] NA NA

## CV term missing
parseCvParameter("[, , user, value]")
#> [1] NA
parseCvParameter("[, , user, value]", 3)
#> [1] "user"
parseCvParameter("[, , user, value]", 4)
#> [1] "value"

## Check validity of CV parameters
isCvParameter(c(x, "[a, b, c, d, e]", "d"))
#> [1]  TRUE  TRUE FALSE FALSE