MultiAssayExperimentToMAF: Convert MultiAssayExperiment to MAF class

In vjcitn/biocMultiAssay: Software for the integration of multi-omics experiments in Bioconductor

Convert MultiAssayExperiment to MAF class

Description

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

vjcitn/biocMultiAssay documentation built on Nov. 24, 2024, 3:04 a.m.