GOxploreR (version 1.2.8)

Gene2GOTermAndLevel: Get the Gene Ontology (GO) terms associated with a gene(s) and their levels

Description

Retrieves the gene association GO-terms, also, the ontology of the terms as well as the respective levels based on the directed acyclic graph (DAG) are returned. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm", "Arabidopsis thaliana / cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".

Usage

Gene2GOTermAndLevel(genes, organism, domain = NULL)

Value

A data.frame object that contains the genes, GO terms, ontology and GO-levels

Arguments

genes

A character vector of entrezgene id's belonging to an organism of interest

organism

An object of class character. A character string that defines the scientific / common name of the organism eg. Homo sapiens, Mouse.

domain

An optional object of class character. GO-terms have three domains .i.e. biological process (BP), molecular function (MF) and cellular component (CC). This character string identifies which of the three GO categories associated with the genes to return. GO-terms from one domain can be returned at a time. If NULL the biological process GO-terms will be obtained (default).

Examples

 # human genes
v <- c(6713,4605,55143,10615,10212,4001,2146,11130,983,4085,9833,9134)

# No value for domain is given so the default ("BP") is used
Gene2GOTermAndLevel(genes = v, organism = "Homo sapiens")

# The scientific names of the species can also be used
Gene2GOTermAndLevel(genes = v, organism = "Homo sapiens", domain = "CC")

Gene2GOTermAndLevel(genes = v, organism = "Human", domain = "MF")