Given a GSEA result, users can be left to wonder which genes are "pushing" the GSEA result one way or the other.
Currently there is an interactive method to explore which the overlap of genes from one geneset to another via code (subsetByFeatures()), or the interactive shiny app provided by multiGSEA.shiny::explore() (by dragging over genes in the GSEA/geneSet plots).
The table of GSEA statistics provided by the result() (results()) function has no gene-level information per geneset, however.
It would be useful to allow the user the option to include the "top n" genes per geneset, perhaps something like:
result(mg.result, "camera", with.features = 5)
would include a "top_features" column in the result table with the concatenation of symbols or ids of the top (or bottom) 5 genes in the geneset.
Given a GSEA result, users can be left to wonder which genes are "pushing" the GSEA result one way or the other.
Currently there is an interactive method to explore which the overlap of genes from one geneset to another via code (
subsetByFeatures()), or the interactive shiny app provided bymultiGSEA.shiny::explore()(by dragging over genes in the GSEA/geneSet plots).The table of GSEA statistics provided by the
result()(results()) function has no gene-level information per geneset, however.It would be useful to allow the user the option to include the "top n" genes per geneset, perhaps something like:
would include a "top_features" column in the result table with the concatenation of symbols or ids of the top (or bottom) 5 genes in the geneset.