Skip to contents

Getting the sampled cells' mutations

Source: R/RcppExports.R
PhylogeneticForest-cash-get_sampled_cell_mutations.Rd

This method returns the mutations of the sample cells.

Arguments

cell_id

The identifier of the cell whose mutations are aimed (optional).

Value

A data frame reporting cell_id, chr, (i.e., the mutation chromosome), chr_pos (i.e., position in the chromosome), allele (in which the mutation occurs), ref, alt, type (i.e., either "SNV" or "indel"), cause, and class (i.e., "driver", "passenger", "germinal" or "preneoplastic") for each mutation in the sampled cell genomes.

Details

This method builds a data frame representing all the SNV and the indel mutations in the cells sampled during the simulation and represented by the leaves of the phylogenetic forest. The data frame also reports the allele in which the mutations occur to support double occurrences due to CNAs.

See also

PhylogeneticForest$$get_sampled_cell_CNAs()

Examples

sim <- TissueSimulation()

sim$add_mutant(name = "Clone_1",
               epigenetic_rates = c("+-" = 0.01, "-+" = 0.01),
               growth_rates = c("+" = 0.2, "-" = 0.08),
               death_rates = c("+" = 0.05, "-" = 0.01))
sim$place_cell("Clone_1+", 500, 500)
sim$run_up_to_size("Clone_1-", 1000)
#> 
 [████████████████████████████████████████] 100% [00m:00s] Saving snapshot                                                                                                             


sim$sample_cells("Sample_A", c(475, 475), c(525, 525))
sample_forest <- sim$get_sample_forest()

m_engine <- MutationEngine(setup_code = "demo")
#> 
 [█---------------------------------------] 0% [00m:00s] Loading context index                                                                                                         

 [████████████████████████████████████████] 100% [00m:00s] Context index loaded                                                                                                        

#> 
 [█---------------------------------------] 0% [00m:00s] Loading RS index                                                                                                              

 [████████████████------------------------] 39% [00m:01s] Loading RS index                                                                                                             

 [███████████████████████████████---------] 76% [00m:02s] Loading RS index                                                                                                             

 [████████████████████████████████████████] 100% [00m:02s] RS index loaded                                                                                                             

#> 
 [█---------------------------------------] 0% [00m:00s] Loading germline                                                                                                              

 [████████████████████████████████████████] 100% [00m:00s] Germline loaded                                                                                                             


m_engine$add_mutant("Clone_1", list("+" = c(SNV = 1e-8, indel = 1e-8),
                                    "-" = c(SNV = 3e-8, CNA = 1e-11)),
                    list(SNV("22", 10510210, "C", allele = 1),
                         CNA("D", "22", 5010000, 200000,
                                   allele = 1)))
#> 
 [█---------------------------------------] 0% [00m:00s] Retrieving "Clone_1" SIDs                                                                                                     

 [████████████████████████████████████████] 100% [00m:00s] "Clone_1"'s SIDs validated                                                                                                  


m_engine$add_exposure(c(ID1 = 1, SBS1 = 0.5, SBS2 = 0.5))

phylo_forest <- m_engine$place_mutations(sample_forest, 1, 1)
#> 
 [█---------------------------------------] 0% [00m:00s] Placing mutations                                                                                                             

 [████████████████████████████████████████] 100% [00m:00s] Mutations placed                                                                                                            


mutations <- phylo_forest$get_sampled_cell_mutations()

head(mutations)
#>   cell_id chr  chr_pos allele   ref alt  type cause     class
#> 1    1119  22 17195209      0 GACTC   G indel   ID1 passenger
#> 2    1119  22 17369333      0     C   T   SNV  SBS2 passenger
#> 3    1119  22 21076747      0     T   C   SNV  SBS2 passenger
#> 4    1119  22 21674289      0     C   T   SNV  SBS1 passenger
#> 5    1119  22 22100524      0  GACT   G indel   ID1 passenger
#> 6    1119  22 22112463      0 GCGTA   G indel   ID1 passenger