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hbctraining / Training-modules

Materials for short, half-day workshops
https://hbctraining.github.io/Training-modules/
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new code for gseKEGG() #19

Open rkhetani opened 3 years ago

rkhetani commented 3 years ago 
gseaKEGG <- gseKEGG(geneList = foldchanges, # ordered named vector of fold changes (Entrez IDs are the associated names)
                    organism = "hsa", # supported organisms listed below
                    #nPerm = 1000, # default number permutations
                    minGSSize = 20, # minimum gene set size (# genes in set) - change to test more sets or recover sets with fewer # genes
                    pvalueCutoff = 0.05, # padj cutoff value
                    verbose = FALSE,
                    eps = 0)