Extract clonal (i.e., truncal) data for a patient.

From a cohort object, this function extracts the tibble of truncal events for a patient (either CCF or binary).

Truncal(x, p)

Arguments

x

A REVOLVER cohort.

p

The id of a patient in the cohort.

Value

Truncal data for a custom patient.

See also

Other Getters: CCF(), CCF_clusters(), Clonal_cluster(), Data(), Drivers(), ITransfer(), Phylo(), Samples(), Subclonal(), get_features()

Examples

# Data released in the 'evoverse.datasets'
data('TRACERx_NEJM_2017_REVOLVER', package = 'evoverse.datasets')

Truncal(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002')
#> # A tibble: 2 × 12
#>   id    Misc  patientID variantID is.driver is.clonal cluster cluster_size CCF  
#>   <chr> <chr> <chr>     <chr>     <lgl>     <lgl>     <chr>          <int> <chr>
#> 1 __mu… CRUK… CRUK0002  MET       TRUE      TRUE      2                  2 R1:0…
#> 2 __mu… Anno… CRUK0002  TERT      TRUE      TRUE      2                  2 R1:0…
#> # ℹ 3 more variables: R1 <dbl>, R2 <dbl>, R3 <dbl>

Truncal(TRACERx_NEJM_2017_REVOLVER, 'CRUK0008')
#> # A tibble: 5 × 11
#>   id    Misc  patientID variantID is.driver is.clonal cluster cluster_size CCF  
#>   <chr> <chr> <chr>     <chr>     <lgl>     <lgl>     <chr>          <int> <chr>
#> 1 __mu… CRUK… CRUK0008  KEAP1     TRUE      TRUE      2                  5 R1:0…
#> 2 __mu… CRUK… CRUK0008  STK11     TRUE      TRUE      2                  5 R1:0…
#> 3 __mu… CRUK… CRUK0008  PRDM1     TRUE      TRUE      2                  5 R1:0…
#> 4 __mu… CRUK… CRUK0008  U2AF1     TRUE      TRUE      2                  5 R1:0…
#> 5 __mu… Anno… CRUK0008  MYC       TRUE      TRUE      2                  5 R1:0…
#> # ℹ 2 more variables: R1 <dbl>, R2 <dbl>