Get all gene symbol in kegg pathway with clusterProfiler

Question

[Peter]

How can we get all genes in a Pathway with clusterProfiler? eg, kegg pathway: hsa04151.

Thank you very much in advance.

Answer 1

[Guangchuang Yu]

using github version:

> bitr_kegg("hsa04151", "Path", "ncbi-geneid", "hsa") 
        Path ncbi-geneid
1   hsa04151       10000
2   hsa04151       10018
3   hsa04151   100533105
4   hsa04151       10110
5   hsa04151       10161
6   hsa04151        1017
7   hsa04151        1019
8   hsa04151        1021
9   hsa04151        1026
10  hsa04151        1027
11  hsa04151   102723407
12  hsa04151       10319
13  hsa04151       10488
,,,

[msimmer92]

@Guangchuang Yu After doing the KEGG pathway analysis with ClusterProfiler and get the dotplot with the pathways, I would like to have a list with the genes so I can take a look (not all the genes in a given pathway, but the specific genes that had appeared in my pathway analysis). How can I do that?