GOSets Class

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.

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.

See also

Sets, GOHits, GOSets-methods.

Examples

# Constructor ----

# Fetch a sample of GO annotations
library(org.Hs.eg.db)
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: IRanges
#> 
go_sets <- import(org.Hs.egGO)
#> Loading required namespace: GO.db
#> 
#> 'select()' returned 1:1 mapping between keys and columns
#> Coercing evidence to factor
#> Coercing ontology to factor
relations <- as.data.frame(head(go_sets))

gs <- GOSets(relations)

# Subsetting ----

gs1 <- subset(gs, element == "1" & ontology == "BP" & evidence == "TAS")
relations(gs1)
#> GOHits object with 2 hits and 2 metadata columns:
#>            from        to | evidence ontology
#>       <integer> <integer> | <factor> <factor>
#>   [1]         1         1 |      TAS       BP
#>   [2]         1         2 |      TAS       BP
#>   -------
#>   nLnode: 1 / nRnode: 2

# Getters/Setters ----

evidence(gs)
#> [1] TAS ND  TAS IDA TAS TAS
#> 26 Levels: EXP IDA IPI IMP IGI IEP HTP HDA HMP HGI HEP IBA IBD IKR IRD ... IEA
ontology(gs)
#> [1] BP BP BP BP BP BP
#> Levels: BP MF CC

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

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