This method returns the known driver mutations.
Details
The mutation are returned in a data frame reporting
the known driver mutations together with their types,
associated tumours, affected genes, and code name. The
first three columns ("chr", "from", and "to")
report the mutation chromosome, the initial position
and the final position, respectively. The next three
columns ("ref", "alt", and "mutation_type")
describe the reference sequence, the altered sequence,
and the type of the mutation. The last four columns
("driver_gene", "driver_code", "driver_CDS", and
"tumour_type") detail the affected gene, the driver
code, which can be used to specify the mutation when
adding a mutant to the mutation engine, the variant code,
and the tumour type associated to the mutation.
Examples
# build a mutation engine
m_engine <- MutationEngine(setup_code = "demo")
#>
[█---------------------------------------] 0% [00m:00s] Loading context index
[████████████████████████████████████████] 100% [00m:00s] Context index loaded
#>
[█---------------------------------------] 0% [00m:00s] Loading RS index
[█████████████████-----------------------] 40% [00m:01s] Loading RS index
[████████████████████████████████--------] 78% [00m:02s] Loading RS index
[████████████████████████████████████████] 100% [00m:02s] RS index loaded
#>
[█---------------------------------------] 0% [00m:00s] Loading germline
[████████████████████████████████████████] 100% [00m:00s] Germline loaded
# get the known driver data frame
head(m_engine$get_known_drivers(), 5)
#> chr from to ref alt mutation_type driver_gene driver_code
#> 1 1 11168260 11168260 G A SNV MTOR MTOR L2538F
#> 2 1 11168260 11168260 G A SNV MTOR MTOR L2538F
#> 3 1 11168260 11168260 G A SNV MTOR MTOR L2538F
#> 4 1 11168260 11168260 G A SNV MTOR MTOR L2538F
#> 5 1 11168260 11168260 G A SNV MTOR MTOR L2538F
#> driver_CDS tumour_type
#> 1 c.7612C>T BLCA
#> 2 c.7612C>T BRCA
#> 3 c.7612C>T CCRCC
#> 4 c.7612C>T CHRCC
#> 5 c.7612C>T CLLSLL