pagoda2 (version 1.0.0)

p2.generate.go: Generate a GO environment for the organism specified

Description

Generate a GO environment for the organism specified

Usage

p2.generate.go(
  r,
  organism = NULL,
  go2all.egs = NULL,
  eg.alias2eg = NULL,
  min.env.length = 5
)

Arguments

r

a 'Pagoda2' object

organism

the organism (default=NULL). Currently 'hs' (human), 'mm' (mouse) and 'dr' (zebrafish) are supported.

go2all.egs

mappings between a given GO identifier and all of the Entrez Gene identifiers annotated at that GO term or to one of its child nodes in the GO ontology (default=NULL)

eg.alias2eg

mappings between common gene symbol identifiers and entrez gene identifiers (default=NULL)

min.env.length

numeric Minimum environment length (default=5)

Examples

# NOT RUN {
cm <- p2data::sample_BM1
p2 <- basicP2proc(cm)
p2.generate.go(p2, organism='hs')
# }
# NOT RUN {
# }