prioritizedGOTerms {GOxploreR}

prioritization of a lists of GO-terms

Description

Given a vector of GO-terms, this function prioritizes the GO-terms by expoiting the structure of a DAG. Starting from the GO-term on the highest level and searching all the paths to the root node iteratively. If any GO-terms in the input vector are found along this path, these GO-terms are removed. This is because the GO-term at the end of a path is more specific than the GO-terms along the path. For an organism, the GO-terms of that organism are used for the prioritization. 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

prioritizedGOTerms(lst = NULL, organism = NULL, sp = TRUE, domain = "BP")

Arguments

lst

The GO ids we want to prioritize

organism

If organism is given then only the gene association GO-terms of that organism are considered during the prioritization otherwise, all the (non-retired) GO-terms from a particular ontology are used in the ranking.

sp

If the argument "sp" is TRUE, only shortest paths are used, otherwise all paths

domain

Ontology of the GO-terms. The default is BP.

Value

A list containing the prioritize GO-terms, their ranking, original GO-terms and their GO-levels is given.

Examples

Terms <-c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415","GO:0006614",
 "GO:0045047","GO:0022411","GO:0001775","GO:0046649","GO:045321")
prioritizedGOTerms(Terms, organism = "Human", sp=TRUE, domain = "BP")