Question: ClusterProfiler can't load gmt file
gravatar for sarah.blackstone7734
19 months ago by
sarah.blackstone77340 wrote:


I am using clusterProfiler, and I would like to load a collection of gmt files to be used for GSEA. However, the instructions given in the vinette are not working for me.


gmtfile <- system.file("extdata", "genesets.gmt", package="clusterProfiler")

c5 <- read.gmt(gmtfile)


I think there is a problem with my use of the system.file() function, because gmtfile is empty:

> gmtfile <- system.file("extdata", "genesets.gmt", package="clusterProfiler")
> gmtfile
[1] ""



I can assure everyone I am in the correct directory.



ClusterProfiler: 2.2.7

qusage: 1.8.7

R: 3.2.1

ADD COMMENTlink modified 19 months ago by Guangchuang Yu950 • written 19 months ago by sarah.blackstone77340
gravatar for Guangchuang Yu
19 months ago by
Hong Kong
Guangchuang Yu950 wrote:

Issue 1:


> rvcheck::check_bioc("clusterProfiler")
devel branch is used, this function only works for release version...
[1] "clusterProfiler"

[1] ‘3.1.5’

[1] "3.0.4"

[1] NA


your R & clusterProfiler are too old.


Issue 2:

gmtfile <- system.file("extdata", "genesets.gmt", package="clusterProfiler")


you need to read the docs by :



Your file, genesets.gmt, is not packed in clusterProfiler, and of course can't be located by system.file.


All you need is something like:


gmtfile <- "path_to_your_file"



ADD COMMENTlink modified 19 months ago • written 19 months ago by Guangchuang Yu950
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