Outdated functions called in the decoupler module in the GSEA chapter

[ginnyintifa]

decoupler.run_gsea() is not a function in recent version anymore.

scores, norm, pvals = decoupler.run_gsea(
    t_stats.T,
    reactome[reactome["geneset"].isin(gsea_genesets)],
    source="geneset",
    target="genesymbol",
)

can be replaced with

net = reactome[reactome['geneset'].isin(gsea_genesets)]
net = net.rename(columns={'geneset' : 'source', 'genesymbol': 'target'})
scores,  pvals= decoupler.mt.gsea(
    t_stats.T,
    net = net
)

and the returns of the function also changed so the downstream needs to be changed as well.

Happy to file a PR.

[LuisHeinzlmeier]

Hi @ginnyintifa,
thanks for raising this issue! I'm going to update the chapter soon.