CVParam-class: Class '"CVParam"'
In rols: An R interface to the Ontology Lookup Service

Description Usage Arguments Objects from the Class Slots Extends Methods Methods Author(s) Examples

CVParam objects instantiate controlled vocabulary entries.

1	CVParam(label, name, accession, value, exact = TRUE)

`label`	A `character` with the ontology label. If missing, a user-defined parameter is created.
`name`	A `character` with the name of the `CVParam` to be constructed. This argument can be omitted if `accession` is used and `label` is not missing.
`accession`	A `character` with the accession of the `CVParam` to be constructed. This argument can be omitted if `name` is used. Ignored for user-defined instances.
`value`	A `character` with the value of the `CVParam` to be constructed. This argument is optional.
`exact`	A `logical` defining whether the query to retrieve the `accession` (when `name` is used) should be an exact match.

Objects can be created with the CVParam constructor.

label:: Object of class "character" that defines the label of the instance, i.e the ontology abbreviation/prefix. See Ontologies to generate a list of available ontologies and olsPrefix for existing labels.
accession:: Object of class "character" with the parameter's valid label ontology accession number. See below for validity constrains.
name:: Object of class "character" with the instance's valid name, i.e matching with the accession. name and accession must follow term(accession, label) == name for the instance to be valid.
value:: Object of class "character" with the CVParams value, if applicable, of empty string ("") otherwise.
user:: Object of class "logical" defining if the instance is a user-defined parameter (also called User params).
.__classVersion__:: Object of class "Versions" describing the instance's class definition version. For development use.

Class "Versioned", directly.

charIsCVParam(x): Checks if x, a character of the form "[ONTO, ACCESSION, NAME, VALUE]", is a valid (possibly user-defined) CVParam. "ONTO" is the ontology label (prefi), "ACCESSION" is the term accession number, "NAME" is the term's name and "VALUE" is the value. Note that only syntax validity is verified, not semantics. See example below.

coerce

signature(from = "CVParam", to = "character"): Coerces CVParam from to a character of the following form: [label, accession, name, value]. as.character is also defined.

coerce

signature(from = "character", to = "CVParam"): Coerces character from to a CVParam. as.CVParam is also defined. If a label is absent, the character is converted to a User param, else, the label and accession are used to query the Ontology Lookup Service (see OlsSearch)). If a name is provided and does not match the retrieved name, a warning is thrown.

This function is vectorised; if the from character is of length greater than 1, then a list of CVParam is returned. The queries to the OLS are processed one-by-one, though.

show

signature(object = "CVParam"): Prints the CVParam instance as text.

rep

signature(x = "CVParam", times = "numeric"): Replicates the CVParam x times times.

Laurent Gatto <lg390@cam.ac.uk>

## a user param
CVParam(name = "A user param", value = "the value")
## a CVParam from PSI's Mass Spectrometry ontology
term("MS", "MS:1000073")
CVParam(label = "MS", accession = "MS:1000073")
CVParam(label = "MS", name ="electrospray ionization")
CVParam(label = "MS", name ="ESI") ## using a synonym

## From a CVParam object to a character
cv <- as(CVParam(label = "MS", accession = "MS:1000073"), "character")
cv

## From a character object to a CVParam
as(cv, "CVParam")
as("[MS, MS:1000073, , ]", "CVParam") ## no name
as("[MS, MS:1000073, ESI, ]", "CVParam") ## name does not match
as(c(cv, cv), "CVParam") ## more than 1 character

x <- c("[MS, MS:1000073, , ]", ## valid CV param
       "[, , Hello, world]",   ## valid User param
       "[this, one is, not, valid]", ## not valid
       "[ , , , ]") ## not valid

stopifnot(charIsCVParam(x) == c(TRUE, TRUE, FALSE, FALSE))

## A list of expected valid and non-valid entries
rols:::validCVchars
rols:::notvalidCVchars