Create a GeneOntologyFilter object

A GeneOntologyFilter object allows for filtering based on gene ontology (GO) terms. Its associated getCandidates method uses an organism database and a GO term (e.g. GO:#######) to filter a list of possible regulators factors to those that match the GO term.

GeneOntologyFilter(
  organismDatabase = org.Hs.eg.db::org.Hs.eg.db,
  GOTerm = "GO:0006351",
  quiet = TRUE
)

Arguments

organismDatabase	An organism-specific database of type 'OrgDb'
GOTerm	A character matching an accepted gene ontology term. The default term corresponds to "transcription, DNA-templated". (default="GO:0006351")
quiet	A logical denoting whether or not the filter should print output

Value

A GeneOntologyFilter object

See also

CandidateFilter

Examples

# Make a filter for "transcription, DNA-templated"
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")'.
goFilter <- GeneOntologyFilter(org.Hs.eg.db, GOTerm="GO:0006351")