Feature Request: topSets enhancements

[jrthompson54]

topSets returns information similar to the stats page in the html report but is missing the NumGenes and Contributor columns. Would like to see these columns also returned by topSets.

If I understand, the NumGenes column correctly, for X/Y numbers, Y corresponds to the number of genes annotated as members of a pathway and X represents the number of those genes present in the input dataset. It would also be useful to report the number of genes regulated based on a settable foldchange/p.adj thresholds. In addition, it would also be useful (perhaps optionally) to return the regulated gene symbols.

Specifically for the KEGG collection, it would be useful if topSets also returns the Type field (metabolism, signaling etc.).

John Thompson (BMS)