hypeR employs multiple types of enrichment analyses (e.g. hypergeometric, kstest, gsea). Depending on the type, different kinds of signatures are expected. There are three types of signatures hypeR() expects.

Geneset

A geneset is simply a list of vectors, therefore, one can use any custom geneset in their analyses, as long as it’s appropriately defined.

genesets <- list "GSET1" = c "GENE1" , "GENE2" , "GENE3" ), "GSET2" = c "GENE4" , "GENE5" , "GENE6" ), "GSET3" = c "GENE7" , "GENE8" , "GENE9" ))

Hyper enrichment All workflows begin with performing hyper enrichment with hyper() . Often we are just interested in a single signature, as described above. In this case, hyper() will return a hyp object. This object contains relevant information to the enrichment results and is recognized by downstream methods. hyp_obj <- hypeR signature , genesets )