GOSets-methods: Methods for 'GOSets' 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 GOSets class. The GOSets class directly extends Sets and thus inherits of all methods defined for the parent class. In the usage below, object represents an object of class inheriting from GOSets, and value is an object of a class specified in the S4 method signature or as outlined in 'Accessors'.

Usage

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

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

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

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

Arguments

object	An object of class inheriting from GOSets.
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

GOSets, Sets-methods.

Examples

# Constructor ----

# Fetch a sample of GO annotations
library(org.Hs.eg.db)
go_sets <- import(org.Hs.egGO)
relations <- as.data.frame(head(go_sets))

gs <- GOSets(relations)

# Accessors ----

evidence(gs)
gs1 <- gs
evidence(gs1)[1] <- "EXP"
ontology(gs)
gs1 <- gs
ontology(gs1)[1] <- "CC"

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