EnrichKegg still shows all pvalues even after specifying a specific pvalue cutoff

[NeginValizadegan]

Although I use pvalueCutoff, the results still show pvalues larger than 0.1. Why is that?

kk2 <- enrichKEGG(gene = dedup_ids_gene$ENTREZID, universe=dedup_ids_bg$ENTREZID, keyType = "ncbi-geneid", organism = kegg_organism, pvalueCutoff = 0.1, pAdjustMethod = "fdr", use_internal_data = FALSE)

[nmclark2]

I am experiencing this same issue for all the enrichment functions. I am currently just filtering the p.adjust column manually, but surely this is not intended?

[huerqiang]

Please provide the kk2 object, and see the result of as.data.frame(kk2).

[nmclark2]

Hello, the as.data.frame() call works to appropriately filter the data matrix for me. To me, this was not clear from the current documentation. Thank you for the explanation.