as_maftools_obj: Convert a CNAqc object to a maftools object.

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Convert a CNAqc object to a maftools object.

Description

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.

Usage

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
}

caravagnalab/CNAqc documentation built on Oct. 31, 2024, 3:54 a.m.