How to assign PAM50 subtypes to RNA seq data?

Question

[bionerd]

Hi, I have RNA-seq data on mouse mammary tumors and I want to see which PAM50 subtype they cluster with. However, I am not really sure how I can do this. Would I use FPKM and just cluster with the 50-gene signature?

thanks

Answer 1

[james.hawley]

Take a look at the molecular.subtyping in the genefu Bioconductor package