Question: BioQC R package issue with broad gmt files
gravatar for Seymoo
12 months ago by
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)`

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

gmt<- getGmt(gmt)`

gmt files can be found here

How can I possibly fix this problem?

ADD COMMENTlink modified 12 months ago • written 12 months ago by Seymoo0

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

ADD REPLYlink written 12 months ago by Seymoo0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 141 users visited in the last hour