Question: BioQC R package issue with broad gmt files
0
gravatar for Seymoo
20 months ago by
Seymoo0
Oslo
Seymoo0 wrote:

I am trying to use a gmt file from broad with wmwTest instead of the gmt file included in the package, but I get `Error in FUN(X[[i]], ...) : index must be either integer vector` in R. I tried to ways of importing the gmt file as below, none were successful.

`gmt <- Sys.glob("E:/files/Rspace/geneset.gmt")
gmt<- read.gmt(gmt)`

and
`gmt <- Sys.glob("E:/files/Rspace/geneset.gmt")

gmt<- getGmt(gmt)`

gmt files can be found here http://software.broadinstitute.org/gsea/downloads.jsp
 

How can I possibly fix this problem?

R gsea gmt bioqc • 322 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by Seymoo0

Problem Solved by using `readGmt`
`gmt <- Sys.glob("E:/files/Rspace/geneset.gmt")`
`gmt <- readGmt(gmt)`

ADD REPLYlink written 20 months ago by Seymoo0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 179 users visited in the last hour