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

Hi,

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.

 

Versions:

ClusterProfiler: 2.2.7

qusage: 1.8.7

R: 3.2.1

ADD COMMENTlink modified 23 months ago by Guangchuang Yu1.0k • written 23 months ago by sarah.blackstone77340
0
gravatar for Guangchuang Yu
23 months ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k wrote:

Issue 1:

 

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

$installed_version
[1] ‘3.1.5’

$latest_version
[1] "3.0.4"

$up_to_date
[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 :

?system.file

 

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 23 months ago • written 23 months ago by Guangchuang Yu1.0k
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