The ORANGES package is a package designed to do over-representation analyses for an omics signature (transcriptomics or proteomics). This is done using the hypergeometric distribution test (or Fisher's exact test) against a collection of pathway gene sets. ORANGES was developed for gene set enrichment of human signatures and the pathway sets were gathered from the Consensus Pathway DataBase.
To install the package do, in R:
devtools::install_github("diogocamacho/oranges")
The easiest way to run the algorithm is to use the oranges wrapper. In R, do:
enrichment <- oranges(query_entrez, universe_entrez)
where query_entrez are the EntrezIDs for the query of interest, and universe_entrez are the EntrezIDs of the background (e.g., the total set of genes identified in the platform of interest). The output of the wrapper is a tidy data frame where columns are source of the pathway set, name of pathway, gene ratio, and nominal and corrected p-values for the test statistic.
Please see the package vignette for a detailed example:
browseVignette("oranges")
For suggestions, comments, additions, please do not hesitate to email me