How to use CP:REACTOME subcategory under category C2 in Broad list (globaltest)
0
0
Entering edit mode
@aditya-saxena-6706
Last seen 3.2 years ago

 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)

Thanks 

globaltest • 637 views
ADD COMMENT

Login before adding your answer.

Traffic: 157 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6