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Question: BioQC R package issue with broad gmt files
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gravatar for Seymoo
9 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?

ADD COMMENTlink modified 9 months ago • written 9 months ago by Seymoo0

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

ADD REPLYlink written 9 months ago by Seymoo0
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