Integration of maftools with CNAqc

[caravagn]

Dear @PoisonAlien, first of all congratulations on this great package (we chatted before on my TRONCO github space).

I would like to interface my new CNAqc package with maftools, and I am unsure on the best way to convert data formats (CNAqc to maf).

CNAqc can QC allele-specific CNAs and mutations calls for a single patient, and contains multiple functions to plot data from a single patient. Sometimes, when I have multiple CNAqc objects from many patients, I wish to plot a cohort-level visualisation of the input data. For CNA segments, I have implemented something pretty canonical. For mutations, however, I would like to interface maftools instead of coding a new visualisation from scratch...

Every CNAqc patient has input mutation data in this format (copying some examples from here, the reference could be either hg19 or GRCh38)

#> # A tibble: 12,963 × 8
#>    chr      from      to ref   alt      DP    NV    VAF
#>    <chr>   <dbl>   <dbl> <chr> <chr> <dbl> <dbl>  <dbl>
#>  1 chr1  1027104 1027105 T     G        60     6 0.1   
#>  2 chr1  2248588 2248589 A     C       127     9 0.0709
#>  3 chr1  2461999 2462000 G     A       156    65 0.417 

and CNA data in this format

#> # A tibble: 267 × 5
#>    chr       from       to Major minor
#>    <chr>    <int>    <int> <dbl> <dbl>
#>  1 chr1    840009  1689987     3     2
#>  2 chr1   1689988  1815015     3     2
#>  3 chr1   1815016  9799969     3     2

I know maftools can parse ANNOVAR annotations, so I am thinking that maybe the best option would be to create a function to annotate with ANNOVAR mutations from a CNAqc input object, and then take it to maftools.

Would you have functions or best practices/ parameters to make this step?

Thanks,

Giulio