Initialise TOSCA object

Usage

init(mutations, parameters, samples, therapies = NULL, sample_name = "Example")

Arguments

mutations: data.frame with the information on mutation falling on the timed branches. 1. Name (str), name of choosing for the cluster of mutations 2. Length (int), length of the genomic segment they sit on 3. Karyptype (str), karyotype of the genomic segment they sit as "Major:minor" (ex "1:1") 4. Type (str), one between the following: "clock-like primary", "clock-like relapse", "alpha", "beta", "driver", the name of the mutagenic drug to which they are associated as reported in the therapies dataframe 5. Value (int), number of mutations
parameters: data.frame with the parameters required for inference. 1. Name (str), 2. Value (real), 3. Index (int)
samples: data.frame with the name and collection date of the longitudinal samples + date of birth (optional). 1. Name (str), name of the sample 2. Date (date) date of collection in the format "YYYY-mm-dd"
therapies: data.frame with the name and exposure period to therapies affecting the mutation accumulation process. 1. Name (str) 2. Class (str), one of the following : "Mutagenic step", "Mutagenic cauchy", "Driver responsive", "Chemotherapy inducing dormancy" 3. Start (date), start of the cicle of therapy in the format "YYYY-mm-dd" 4. End (date), end of the cicle of therapy in the format "YYYY-mm-dd"
sample_name: string with the name of the sample

Value

TOSCA object

Examples

library(TOSCA)
library(dplyr)
library(ggplot2)
data("exampleData_CNA")
mutations = exampleData_CNA$Mutations
parameters = exampleData_CNA$Parameters
samples = exampleData_CNA$Samples
therapies = exampleData_CNA$Therapies

x = init(mutations=mutations, samples=samples, therapies=therapies, parameters=parameters)
#> Error in init(mutations = mutations, samples = samples, therapies = therapies,     parameters = parameters): Input must be a data.frame.