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