FES: FES
In jhart99/gseasier: Run the GSEA java pacakage from inside R

Description Usage Arguments Value

FES(Fast Enrichment Score or Fisher Enrichment Score) uses a different method of calculating the enrichment score as compared with GSEA. In FES, the hypergeometric distribution is used to determine the p-value for the partitioning of members of the geneset within the ordered valued gene ranking. Two different p-values are calculated from the opposite ends of the ranking to measure enrichment at either the high or low ends of the spectrum. The use of the hypergeometric distribution rather than the complicated method used in GSEA means this method is very fast and yields results which are similar to GSEA itself. In comparison to GSEA, FES is more sensitive to concentration of geneset members in the middle of the ranking as happens with GSEA v1 and is avoided by GSEA v2. All results from FES or GSEA should be evaluated by looking at the plots and changes in gene expression to evaluate the feasibility of detecting the shift in the gene set distribution using experimental tools. Typically if the changes are smaller than a 0.5 on the log2FC scale, they will be challenging to detect by methods such as Q-PCR.

1	FES(sn.table, geneset, hits.only = TRUE)

`sn.table`	a table of ordered, valued gene rankings
`geneset`	a set of genes to determine the FES score
`hits.only`	Emit all genes(False) or only those which are in the geneset(True)