i want to use gt.Broad function from global test package, I have downloaded msigdb_v5.1.xml file and prepare broad collection using GSEABase.
I want to test only Reactome gene sets for my phenotype "x" and Expression set "y". kindly let me know the format for gtBroad function, as reactome gene sets come under subcategory of CP:REACTOME in category C2 of Broadset. can anybody correct given expression to make it executable ?
gtBroad(x, y, category="c2", ??subset="cp:reactome"??, collection=broad)