phenotype: Phenotype Objects

In xu-hong/rphenoscape: Semantically Rich Phenotypic Traits from the Phenoscape Knowledgebase

Phenotype Objects

Description

as.phenotype creates an object (or a list of objects) of type "phenotype". The object to be coerced can be a character vector (of IRIs), or a data.frame. In the latter case, there must be a column "id" with the IRIs of phenotypes. If the object is already of type "phenotype", it is passed through unchanged.

is.phenotype tests whether an object is of type "phenotype"

is_valid_phenotype tests which of the objects in the list are valid phenotype objects, and returns a logical vector of the same length as x. An object is a valid phenotype object if it is of type "phenotype" and its ID has been found in the database.

charstates extracts the character states from the phenotype object (or an object coercible to phenotype)

chars extracts the (non-redundant) characters from the phenotype object (or an object coercible to phenotype).

print pretty-prints objects of type "phenotype"

Usage

as.phenotype(x, withTaxa = FALSE, ...)

## S3 method for class 'data.frame'
as.phenotype(x, ...)

is.phenotype(x)

is_valid_phenotype(x)

charstates(x)

chars(x)

## S3 method for class 'phenotype'
print(x, ...)

Arguments

x	an object of type "phenotype" or coercible to it, or to be tested for being of type "phenotype"
withTaxa	logical. If TRUE taxa exhibiting the phenotype will be available through the phenotype object at key "taxa". Default is FALSE, because obtaining taxa requires an additional query per object.
...	additional parameters where applicable; ignored for printing

Details

Create and test objects of type "phenotype", and extract properties from them.

Value

as.phenotype returns an object of type "phenotype", or a list of such objects if the object to be coerced had multiple elements (if a vector) or rows (if a data.frame). A phenotype object has properties "id" (ID, i.e., IRI of the phenotype), "label" (label of the phenotype if one exists), "states" (a data.frame of the character states to which the phenotype is linked, see value for charstates), and "eqs" (the EQ expression components as a list with keys "entities", "qualities", and "related_entities"). If withTaxa is TRUE, there will also be a key "taxa" (a data.frame with columns "id" and "label").

is.phenotype returns TRUE if the object is of type "phenotype" and FALSE otherwise.

is_valid_phenotype returns a logical vector of the same length as the input array of objects, with TRUE for those objects in the list that are of type "phenotype" and correspond to a phenotype in the database.

charstates returns a data.frame. If called with a single phenotype object (or an object that coerces to one), the data.frame has columns "id" and "label" (for the character state), "character.id" and "character.label" (IRI and label of the character), and "study.id" and "study.label" (IRI and short label for the study to which the character and state belong). If called with a list of phenotype objects (or objects that coerce to such a list), the data.frame will include the character states from all phenotypes in the list. In this case, the character state columns will be "state.id" and "state.label", respectively, and there will be two additional columns, "phenotype.id" and "phenotype.label".

chars returns a data.frame with collumns "character.id" and "character.label" (IRI and label of the character), and "study.id" and "study.label" (IRI and short label for the study to which the character and state belong).

Examples

# query for a set of phenotypes (IDs and their labels)
phens <- get_phenotypes(entity = "basihyal bone")
nrow(phens)
# turn one into a phenotype object
obj <- as.phenotype(phens[3, "id"])
class(obj)
obj

# optionally include taxa exhibiting the phenotype
as.phenotype(phens[3,], withTaxa = TRUE)
# full list of taxa:
as.phenotype(phens[3,], withTaxa = TRUE)$taxa

# can also coerce entire list at once
objs <- as.phenotype(phens)
class(objs)
length(objs)
all(sapply(objs, is.phenotype))
objs[[3]]

# extract character states and (non-redundant) characters
charstates(obj)
chars(obj)

# IDs that don't resolve still yield an object, but is not valid
suppressWarnings(obj <- as.phenotype("http://foo"))
is.phenotype(obj)
is_valid_phenotype(obj)

xu-hong/rphenoscape documentation built on Jan. 28, 2024, 12:22 p.m.