This method returns the available indel signatures.
Details
The signatures are returned in a data frame containing the available indel signatures together with the corresponding mutation probability. The first column ("Type") describes a mutation in a context, while each of the remaining columns contains the probabilities of the mutations for one of the available indel signatures.
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
[█████████████████████████████-----------] 72% [00m:02s] Loading RS index
[████████████████████████████████████████] 100% [00m:02s] RS index loaded
#>
[█---------------------------------------] 0% [00m:00s] Loading germline
[████████████████████████████████████████] 100% [00m:00s] Germline loaded
# get the indel data frame
head(m_engine$get_indel_signatures(), 5)
#> Type ID1 ID2 ID3 ID4 ID5 ID6
#> 1 1:Del:C:0 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 2 1:Del:C:1 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 3 1:Del:C:2 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 4 1:Del:C:3 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 5 1:Del:C:4 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> ID7 ID8 ID9 ID10 ID11 ID12 ID13
#> 1 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 2 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 3 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 4 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 5 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> ID14 ID15 ID16 ID17 ID18 ID19 ID20
#> 1 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 2 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 3 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 4 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> 5 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819 0.01204819
#> ID21 ID22 ID23
#> 1 0.01204819 0.01204819 0.01204819
#> 2 0.01204819 0.01204819 0.01204819
#> 3 0.01204819 0.01204819 0.01204819
#> 4 0.01204819 0.01204819 0.01204819
#> 5 0.01204819 0.01204819 0.01204819