Convert a CNAqc object to a maftools object.

A single CNAqc object for which MAF annotations have been added using function augment_with_maf, can be converted as an object for the Bioconductor package [maftools](https://bioconductor.org/packages/release/bioc/html/maftools.html).

The export will use only driver mutations data or all the annotated mutations, depending on the input flag `only_drivers`. Moreover, CNAqc copy number states of a list of desired genes can also be augmented to the [maftools](https://bioconductor.org/packages/release/bioc/html/maftools.html) object.

as_maftools_obj(
  x,
  only_drivers = TRUE,
  CNA_genes = NULL,
  cross_reference = TRUE,
  assembly = TRUE
)

Arguments

x

A CNAqc object with MAF annotations.

only_drivers

If `TRUE`, only driver mutations are used, otherwised all. When `TRUE`, if drivers are not annotated, an error is thrown.

CNA_genes

The list of genes for ....

assembly

If `TRUE`...

See also

function augment_with_maf to add MAF annotations to a CNAqc object, to be used before running `as_maftools_obj`.

Examples

if(FALSE)
{
   # Create your CNAqc object (omissis here) from an original "file.vcf"
   x = init(mutations = ..., cna = ..., purity = ...)

   # Offline, create your MAF annotations as file "file_vcf.maf" from "file.vcf"
   # vcf2maf file.vcf .... file_vcf.maf

   # Import into R/CNAqc
   x = augment_with_maf(x, maf = "file_vcf.maf")

   # Extraction
   x %>% as_maftools_obj
}