CVParam: Controlled Vocabulary

In lgatto/rols: An R interface to the Ontology Lookup Service

Controlled Vocabulary

Description

'CVParam' objects instantiate controlled vocabulary entries.

Usage

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

## S4 method for signature 'CVParam'
show(object)

## S4 method for signature 'CVParam'
rep(x, times)

Arguments

label	'character(1)' with the ontology label. If missing, a user-defined parameter is created.
name	'character(1)' with the name of the 'CVParam' to be constructed. This argument can be omitted if 'accession' is used and 'label' is not missing.
accession	'character(1)' with the accession of the 'CVParam' to be constructed. This argument can be omitted if 'name' is used. Ignored for user-defined instances.
value	'character(1)' with the value of the 'CVParam' o be constructed. This argument is optional.
exact	'logical(1)' defining whether the query to retrieve the 'accession' (when 'name' is used) should be an exact match.
object	'CVParam' object.
x	'CVParam' to be repeated.
times	'numeric(1)' defining the number of repetitions.

Methods

- '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 (prefix), '"ACCESSION"' is the term accession number, '"NAME"' is the term's name and '"VALUE"' is the value. Note that only the syntax validity is verified, not the semantics. See example below.

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

- 'coerce(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.

Author(s)

Laurent Gatto

Examples

## User param
CVParam(name = "A user param", value = "the value")
## CVParam ESI from PSI's Mass Spectrometry ontology
olsTerm("GO", "GO:0035145")
(eej <- CVParam(label = "GO", accession = "GO:0035145"))
class(eej)

## From a CVParam object to a character
cv <- as(eej, "character")
cv ## note the quotes

## From a character object to a CVParam
as(cv, "CVParam")
as("[GO, GO:0035145, , ]", "CVParam") ## no name
as("[GO, GO:0035145, exon-exon junction complex, ]", "CVParam")
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

lgatto/rols documentation built on April 29, 2024, 12:20 p.m.