GOSets-class: GOSets Class

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

Description

The GOSets class extends the Sets class to implement a container that also describes relations between genes and sets using the Gene Ontology controlled vocabulary. Refer to GOOntologyCodes and GOEvidenceCodes for valid vocabulary.

Usage

GOSets(relations = DataFrame(element = character(0), set = character(0),
  ontology = factor(character(0), names(GOOntologyCodes)), evidence =
  factor(character(0), names(GOEvidenceCodes))), ...)

Arguments

relations	DataFrame. At least 3 columns that provide mapping relationships between "element" and "set", with "membership" function in the range [0,1]. Additional columns are taken as relation metadata.
...	Arguments passed to the Sets() constructor and other functions.

Value

A GOSets object.

Author(s)

Kevin Rue-Albrecht

See Also

Sets, GOHits, GOSets-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)

# Subsetting ----

gs1 <- subset(gs, element == "1" & ontology == "BP" & evidence == "TAS")
relations(gs1)

# Getters/Setters ----

evidence(gs)
ontology(gs)

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

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

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