characterizeDB: characterizeDB

In randomGODB: Random GO Database

characterizeDB

Description

compute distribution of GO category sizes, and fraction of a leaf's ancestors containing a bait gene

Usage

characterizeDB(
  GOGOA3,
  ontology = "biological_process",
  ngene = 2,
  GOBPCHILDREN,
  GOBPANCESTOR,
  hitters = "all",
  verbose = TRUE
)

Arguments

GOGOA3	return value of minimalistGODB::buildGODatabase()
ontology	character c("biological_process","molecular_function","cellular_component")
ngene	integer number of genes to examine within range of 'hitters'
GOBPCHILDREN	GO.db data set
GOBPANCESTOR	GO.db data set
hitters	character c("big","mid","lo","all") designate which portion of gene table to look at
verbose	BOOLEAN if TRUE print out some information

Value

returns the sorted number of GO category sizes, and also has side effect of printing out some information

Examples

## Not run: 
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
ontology<-"biological_process"
t<-characterizeDB(GOGOA3,ontology,ngene=3,GO.db::GOBPCHILDREN,GO.db::GOBPANCESTOR,hitters="all")

## End(Not run)

randomGODB documentation built on June 8, 2025, 9:32 p.m.