Performs GO terms enrichment analyses.
gorilla(target, background = NULL, mode = 'mhg', db = 'proc', pv = 0.001, spe = NULL)path to the txt file containing (one per line) the UniProt id of the proteins belonging to the target set.
path to the txt file containing (one per line) the UniProt id of the proteins belonging to the background set.
a character string specifying the desired analysis mode; it must be one of 'mhg' (identifies enriched GO terms in ranked lists), 'hg' (identifies enriched GO terms in the target set compared to the background set)
a character string specifying the chosen ontology; it must be one of 'proc' (biological process), 'func' (molecular function), 'comp' (cellular component), 'all' (all the three previous ontologies).
a numeric value for the p-value threshold. Only GO terms with a p-value better than this threshold are reported.
a character string specifying the organism of interest. The species supported by GOrilla are: (Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Rattus norvegicus)
Returns either a dataframe with the enrichment results if a single ontology has been selected, or a list with three dataframe if the three ontologies were selected.
This function is a client of GOrilla, which is a web-based application that identifies enriched GO terms.
Eden et al. (2009) BMC Bioinformatics 10:48.
Rhee et al. (2008) Nature Reviews Genetics 9:509<U+2013>515.
search.go(), term.go(), get.go(), bg.go(), net.go()
# NOT RUN {
gorilla(target = './go/GOvivo.txt', db = 'all')
# }
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