R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005
ris used to compute enrichment score (credit to Michael from Berkeley).
charactervectors, named by GO term, of genes associated with each term - can be loaded with
data(GO_gene_sets)[based on Gene Ontology (2015-11-27) and human GO annotations file validated on 07/08/2016]).
gsetis interpreted when vector of scores
ris supplied - now instead of the scores for
Sbeing those at the corresponding ranks in
r, they are those at corresponding indices. For example, in version 1.0 the scores for
S=1:3would be the top 3 scores in
r, however now it be the those of the first 3 elements of
r. Behaviour has not changed for when
Nis used instead of