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 (default "maf_syn").

nonSynAssay

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

Value

A MAF class object

See also

?maftools::MAF