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Merging results from GSEA analysis and ridgeplot for multiple databases

Open GACGAMA opened this issue 2 years ago • 0 comments

Hello! I've been trying to merge multiple gseaResult objects such as those from KEGG, Reactome and Wikipathways to generate one ridgeplot only, for an article

I've done:

reactomegsea <- gsePathway(DE_results_dataframe, 
                  pvalueCutoff = 0.05,
                  pAdjustMethod = "BH", 
                  verbose = FALSE)

and such for KEGG and wikipathways then,

gsea = merge_result(list(A= wikipathwaysgsea , B= KEGGgsea, C= reactomegsea ))
dotplot(gsea)

Which generates the correct dotplot. But I can't generate

p3 <- ridgeplot(gsea, showCategory=50, orderBy="NES") 

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘ridgeplot’ for signature ‘"compareClusterResult"

Of course, the merge_results seems to drop some data (I think it is the gene list and expression) which makes the ridgeplot uncomputable.

Is there any way to merge the gseaResult objects or use any other data do make the ridgeplots?

GACGAMA avatar Jun 29 '22 17:06 GACGAMA