This methods places mutations on a samples forest.
Arguments
- samples_forest
A samples forest.
- num_of_preneoplatic_SNVs
The number of pre-neoplastic SNVs.
- preneoplatic_SNV_signature_name
The name of the SNV signature for the preneoplastic SNV generation (optional).
- num_of_preneoplatic_indels
The number of pre-neoplastic indels.
- preneoplatic_indel_signature_name
The name of the indel signature for the preneoplastic indel generation.
- seed
The seed for random number generator (optional).
Details
Each node of a samples forest is labelled by the mutations occuring in the cell represented by the node itself and produces a phylogenetic forest.
Examples
# set the seed of the random number generator
set.seed(0)
# create a simulation
sim <- SpatialSimulation()
sim$add_mutant("A", c(SNV = 0.2), 0.01)
sim$place_cell("A", 500, 500)
sim$death_activation_level <- 100
sim$run_up_to_size(species = "A", num_of_cells = 50000)
#>
[████████████████████████████████████████] 100% [00m:00s] Saving snapshot
# sample the region [450,500]x[475,550]
sim$sample_cells("S1", lower_corner = c(450, 475),
upper_corner = c(500, 550))
# build the samples forest
samples_forest <- sim$get_samples_forest()
# 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
[███████████████████---------------------] 46% [00m:01s] Loading RS index
[████████████████████████████████████----] 89% [00m:02s] Loading RS index
[████████████████████████████████████████] 100% [00m:02s] RS index loaded
#>
[█---------------------------------------] 0% [00m:00s] Loading germline
[████████████████████████████████████████] 100% [00m:00s] Germline loaded
# add the mutant "A" to the engine
m_engine$add_mutant("A", c(SNV = 3e-9), list(SNV("22", 12028576, "G")))
#>
[█---------------------------------------] 0% [00m:00s] Retrieving "A" SNVs
[█---------------------------------------] 0% [00m:00s] Found 22
[█---------------------------------------] 0% [00m:00s] Reading 22
[█---------------------------------------] 0% [00m:01s] Reading 22
[████████████████████████████████████████] 100% [00m:01s] "A" SNVs retrieved
# add the default set of SNV signature coefficients
m_engine$add_exposure(c(SBS13 = 0.3, SBS1 = 0.7, ID2 = 0.3, ID21 = 0.5,
ID3 = 0.2))
# place the mutations on the samples forest assuming 1000 pre-neoplastic
# SNVs and 500 indels
phylogenetic_forest <- m_engine$place_mutations(samples_forest, 1000, 500)
#>
[█---------------------------------------] 0% [00m:00s] Placing mutations
[████████--------------------------------] 18% [00m:01s] Placing mutations
[███████████████-------------------------] 36% [00m:02s] Placing mutations
[██████████████████████------------------] 54% [00m:03s] Placing mutations
[█████████████████████████████-----------] 72% [00m:04s] Placing mutations
[█████████████████████████████████████---] 90% [00m:05s] Placing mutations
[████████████████████████████████████████] 100% [00m:05s] Mutations placed
phylogenetic_forest
#> PhylogeneticForest
#> # of trees: 1
#> # of nodes: 12267
#> # of leaves: 3868
#> samples: {"S1"}
#>
#> # of emerged SNVs and indels: 1501
#> # of emerged CNAs: 0
#>