Combining compareCluster with enricher in clusterProfiler
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JD ▴ 10
@jd-9512
Last seen 6.0 years ago

Hello,

In the tutorial for clusterProfiler, it mentions that the universal enricher function can be combined with the biological theme compareCluster function:

"The comparison function was designed as a framework for comparing gene clusters of any kind of ontology associations, not onlygroupGOenrichGOenrichKEGG and enricher provided in this package, but also other biological and biomedical ontologies"

I have used enricher on MSigDB .gmt files that I downloaded and it works great. I am stuck on how to combine enricher with compareCluster

- Should I run enricher separately, and then somehow pass those results to compareCluster?

- Or can the enricher call be included as an argument to compareCluster?

- Or are both of those wrong?!

If you have an example I would greatly appreciate it. Because of my Mac OS, I am stuck using:

R 3.3, Bioconductor 3.2, ClusterProfiler 2.4.3

Thank you for creating and sharing clusterProfiler ! The compatibility with so many types of ontologies and the visual enhancements over other ontology tools are wonderful!

JD

clusterprofiler • 1.4k views
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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 11 months ago
China/Guangzhou/Southern Medical Univer…

you can pass fun='enricher' to compareCluster and it works in a similar way of passing fun='enrichGO' or fun='enrichKEGG'.

BTW: you need to upgrade Bioconductor and clusterProfiler

> require(rvcheck)
> check_bioc('clusterProfiler')
## clusterProfiler is out of date...
## try http:// if https:// URLs are not supported
source("https://www.bioconductor.org/biocLite.R")
biocLite("clusterProfiler")
$installed_version [1] ‘3.0.2’$latest_version
[1] "3.0.3"

\$up_to_date
[1] FALSE