Questions on MutSig use

Dear MutSig team,
I have read protocol of MutSig and two relevant papers, to my knowledge; MutSig is mainly developed to identify higher mutated coding genes in human genome, as our research interests are to find highly mutated non coding genes in cancers, such as lncRNAs or miRNAs, could it be possible for us to use MutSig to do this analysis? Thank you so much for your answer.
LI Jia