Question: BioQC R package issue with broad gmt files
0
2.2 years 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)

How can I possibly fix this problem?

R gsea gmt bioqc • 363 views
modified 2.2 years ago • written 2.2 years ago by Seymoo0

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