This method returns the known driver mutations.
Details
The mutation are returned in a dataframe 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 three columns
("tumour_type", "driver_gene", and "driver_code")
detail the tumour type associated to the mutation, the
affected gene, and the driver code, which can be used
to specify the mutation when adding mutants to the
mutation engine.
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
[███████████████-------------------------] 37% [00m:01s] Loading RS index
[███████████████████████████████---------] 75% [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 dataframe
head(m_engine$get_known_drivers(), 5)
#> chr from to ref alt mutation_type tumour_type driver_gene
#> 1 1 115256502 115256508 TGGTCTC - indel PACA NRAS
#> 2 1 115256502 115256508 TGGTCTC - indel PACA NRAS
#> 3 1 115256528 115256528 T G SNV MALY NRAS
#> 4 1 115256529 115256529 T C SNV MELA NRAS
#> 5 1 115256528 115256528 T G SNV MALY NRAS
#> driver_code
#> 1 NRAS RDQ68
#> 2 NRAS A66
#> 3 NRAS Q61H
#> 4 NRAS Q61R
#> 5 NRAS Q61K