GOHits-methods: Methods for 'GOHits' Objects

In kevinrue/unisets: Collection of Classes to Store Gene Sets

Description

This page documents the S4 generics and methods defined for objects inheriting of the GOHits class. The GOHits class directly extends Hits and thus inherits of all methods defined for the parent class. In the usage below, object represents an object of class inheriting from GOHits, and value is an object of a class specified in the S4 method signature or as outlined in 'Accessors'.

Usage

ontology(object)

ontology(object) <- value

evidence(object)

evidence(object) <- value

## S4 method for signature 'GOHits'
evidence(object)

## S4 replacement method for signature 'GOHits'
evidence(object) <- value

## S4 method for signature 'GOHits'
ontology(object)

## S4 replacement method for signature 'GOHits'
ontology(object) <- value

Arguments

object	An object of class inheriting from GOHits.
value	An object of a class specified in the S4 method signature or as outlined in 'Accessors'.

Accessors

evidence(object) returns a factor indicating the evidence code for each relation.

ontology(object) returns a factor indicating the ontology code for each relation.

Author(s)

Kevin Rue-Albrecht

See Also

GOHits, Hits.

Examples

# Controlled vocabulary ----

GOEvidenceCodes
GOOntologyCodes
# Constructor ----

from <- c(5, 2, 3, 3, 3, 2)
to <- c(11, 15, 5, 4, 5, 11)
ontology <- factor(c("BP", "BP", "BP", "MF", "MF", "CC"))
evidence <- factor(c("IEA", "IDA", "IEA", "IDA", "IEA", "IDA"))

gh <- GOHits(from, to, evidence, ontology, 7, 15)
gh

# Accessors ----

evidence(gh)
gh1 <- gh
evidence(gh1)[1] <- "HTP"
ontology(gh)
gh1 <- gh
ontology(gh1)[1] <- "MF"

kevinrue/unisets documentation built on May 15, 2020, 10:48 p.m.