revolver_cohort: Construct a REVOLVER cohort.

In caravagn/revolver: REVOLVER - Repeated Evolution in Cancer

Construct a REVOLVER cohort.

Description

Construct a REVOLVER cohort.

Usage

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)

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

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

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

caravagn/revolver documentation built on May 21, 2022, 5:48 p.m.