Construct a REVOLVER cohort.

Source: R/revolver_cohort.R

Construct a REVOLVER cohort.

revolver_cohort(
  dataset,
  CCF_parser = revolver::CCF_parser,
  ONLY.DRIVER = FALSE,
  MIN.CLUSTER.SIZE = 10,
  annotation = "My REVOLVER dataset"
)

Arguments

dataset

A dataframe in the specified format (see the package vignettes).
CCF_parser

A function to parse the format for the encoding of CCF or binary values for each sequenced region. A possible function is available inside REVOLVER; CCF_parser (the default of this parameter).
ONLY.DRIVER

If true, uses only annotated driver events.
MIN.CLUSTER.SIZE

Discard clusters that have less than this number of entries.
annotation

Brief cohort description.

Value

An object of the S3 class "rev_cohort" that represents a REVOLVER cohort.

See also

Other Cohort creation: CCF_parser(), compute_clone_trees(), compute_mutation_trees(), input_custom_trees(), revolver_check_cohort()

Examples

# Example cohort creation with the TRACERx data
data(TRACERx_data)

#> Warning: data set ‘TRACERx_data’ not found

# To speed up the process we use only 2 patients
TRACERx_data = TRACERx_data %>%
   filter(patientID %in% c('CRUK0001', 'CRUK0002'))

#> Error in filter(., patientID %in% c("CRUK0001", "CRUK0002")): object 'TRACERx_data' not found

cohort = revolver_cohort(TRACERx_data, annotation = 'A toy REVOLVER dataset')

#>  [ REVOLVER ~ Cohort constructor ] 
#> 
#> ℹ Using only driver mutations. 
#> ℹ Rejecting clusters with less than 10 mutations. 
#> Error in lapply(X = X, FUN = FUN, ...): object 'TRACERx_data' not found

# The S3 print/ plot for this cohort
print(cohort)

#> Error in print(cohort): object 'cohort' not found
plot(cohort)

#> Error in plot(cohort): object 'cohort' not found