simulate_generator {CIMICE} | R Documentation

## Create datasets from generators

### Description

Simulate the DTMC associated to the generator to create a dataset that reflects the genotypes of 'times' cells, sampled after 'time_ticks' passages.

### Usage

    simulate_generator(
      generator,
      time_ticks,
      times,
      starting_label = "Clonal",
      by = "labels",
      mode = "full"
    )

### Arguments

`generator` | a generator
`time_ticks` | number of steps (updates) of the DTMC associated to the generato
`times` | number of sumlated cells
`starting_label` | node from which to start the simulation
`by` | "labels" or "samples" to use gene labels or sample labels as references to identify the ‘starting_label'’s node
`mode` | "full" to generate a matrix with 'times' genotypes, "compacted" to *efficiently* create an already compacted dataset (a dataset showing the genotypes and their respective frequencies)

### Value

the simulated dataset

### Examples

    require(dplyr)

    example_dataset() %>%
      make_generator_stub() %>%
      set_generator_edges(
        list(
          "D", "A, D", 1 ,
          "A", "A, D", 1 ,
          "A, D", "A, C, D", 1 ,
          "A, D", "A, B, D", 1 ,
          "Clonal", "D", 1 ,
          "Clonal", "A", 1 ,
          "D", "D", 1 ,
          "A", "A", 1 ,
          "A, D", "A, D", 1 ,
          "A, C, D", "A, C, D", 1 ,
          "A, B, D", "A, B, D", 1 ,
          "Clonal", "Clonal", 1
      )) %>%
      finalize_generator %>%
      simulate_generator(3, 10)

[Package CIMICE version 1.2.1 Index]