first of all, you should tag your post with the package name, clusterProfiler. Only in this way, I can receive email notification.
kk <- enrichKEGG(gene = gene,
organism = "human",
pvalueCutoff = 0.05,
readable = TRUE,
use_internal_data = FALSE)
If you run this code, you should get the following error:
Error in enrichKEGG(gene = gene, organism = "human", pvalueCutoff = 0.05, :
unused argument (readable = TRUE)
since there is no readable argument for enrichKEGG.
I run your code without the readable argument, it works fine and gives the following result:
> head(summary(kk))
ID Description GeneRatio BgRatio
hsa04110 hsa04110 Cell cycle 11/84 124/7081
hsa04114 hsa04114 Oocyte meiosis 10/84 123/7081
hsa03320 hsa03320 PPAR signaling pathway 7/84 72/7081
hsa04914 hsa04914 Progesterone-mediated oocyte maturation 6/84 98/7081
hsa04115 hsa04115 p53 signaling pathway 5/84 69/7081
hsa04062 hsa04062 Chemokine signaling pathway 8/84 187/7081
pvalue p.adjust qvalue
hsa04110 1.915578e-07 3.218171e-05 3.165745e-05
hsa04114 1.616186e-06 1.357596e-04 1.335480e-04
hsa03320 2.029899e-05 1.136744e-03 1.118225e-03
hsa04914 1.026096e-03 4.309603e-02 4.239396e-02
hsa04115 1.291558e-03 4.339635e-02 4.268939e-02
hsa04062 1.598654e-03 4.476231e-02 4.403310e-02
geneID Count
hsa04110 8318/991/9133/890/983/4085/7272/1111/891/4174/9232 11
hsa04114 991/9133/983/4085/51806/6790/891/9232/3708/5241 10
hsa03320 4312/9415/9370/5105/2167/3158/5346 7
hsa04914 9133/890/983/4085/891/5241 6
hsa04115 9133/6241/983/1111/891 5
hsa04062 3627/10563/6373/4283/6362/6355/9547/1524 8
For the second issue, the function is not exported.