Convert MultiAssayExperiment to MAF class

Take a MultiAssayExperiment object with specific mutation assays and convert these into a maftools representation. The names provided via synAssay and nonSynAssay must match exactly those assays in the MultiAssayExperiment.

Usage

MultiAssayExperimentToMAF(x, synAssay = "maf_syn", nonSynAssay = "maf_nonSyn")

Arguments

x

A MultiAssayExperiment object

synAssay

character(1) The name of the ExperimentList element in the MultiAssayExperiment that identifies synonymous variant classifications.

nonSynAssay

character(1) The name of the ExperimentList element in the MultiAssayExperiment that identifies non-synonymous variant classifications.