Get tumourevo formatted CNA (cna2cnaqc) file paths
Usage
get_tumourevo_cna(spn, coverage, purity, vcf_caller, cna_caller, sample = NULL)
Arguments
- spn
SPN identifier, e.g. "SPN01".
- coverage
Sequencing coverage (integer).
- purity
Sample purity: 0.9, 0.6, or 0.3.
- vcf_caller
VCF caller: "mutect2" or "strelka".
- cna_caller
CNA caller: "ascat" or "sequenza".
- sample
Sample name. If NULL, returns paths for all samples.
Value
Named list of file paths to CNA RDS files.
Examples
if (FALSE) { # \dontrun{
get_tumourevo_cna("SPN04", 50, 0.6, "mutect2", "sequenza", "SPN04_1.1")
} # }
