fractAncest: fractAncest

In randomGODB: Random GO Database

fractAncest

Description

analysis of fraction of ancestor categories to which a leaf gene maps

Usage

fractAncest(
  genes,
  GOGOA3,
  ontology = "biological_process",
  GOBPCHILDREN,
  GOBPANCESTOR,
  verbose = TRUE
)

Arguments

genes	character vector list of gene names
GOGOA3	return value of minimalistGODB::buildGODatabase()
ontology	character c("biological_process","molecular_function","cellular_component")
GOBPCHILDREN	GO.db data set
GOBPANCESTOR	GO.db data set
verbose	Boolean if TRUE print out some information

Value

returns no values, but has side effect of printing out some results

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"
genes<-c("CDC45","CELF2")
fractAncest(genes,GOGOA3,ontology,GO.db::GOBPCHILDREN,GO.db::GOBPANCESTOR)

## End(Not run)

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