creating a data file for GSVA analysis

Question

[Sathya]

I would like to use GSVA for enrichment analysis. By default, GSVA uses c2BroadSets data. Instead of c2BroadSets, I wanted to use c7Broadsets which is immune specific enrichment data. How to proceed with this?

Note: There are few blogs which talks about creating c5data using the gmt file available in molecular signature database. But, I have no clue how to proceed with that. Please let me know.

[balli.dave]

Any update on this, Sathya? I actually would like to do the exact same analysis with the C7Broadset.

thanks,

David

Answer 1

[dpenaherrera]

You have to first go to the MSigDB downloads page. Once you login, scroll down to the section labelled "c7: immunologic signatures gene sets" and download the appropriate .gmt file. Then import the data into R with a command similar to the following:

myC7 <- getGmt("c7.all.v5.1.entrez.gmt")

If you get an error, you might need to specify the other parameters of getGmt:

myC7 <- getGmt("c7.all.v5.1.entrez.gmt", geneIdType=EntrezIdentifier(), collectionType=BroadCollection(category="c7"), sep="\t")