tests/testthat/test-One_step_clustering.R

context("Clustering quality and options")

test_that("Check optim",{
  expect_identical(Compute_NMI(
    QuantumClone::One_step_clustering(Input_Example,contamination = c(0,0),nclone_range = 3:5,optim = "default",save_plot= FALSE,preclustering = "FLASH")
  ), 1)
  
})
test_that("Check optimx",{
  expect_identical(Compute_NMI(
    QuantumClone::One_step_clustering(Input_Example,contamination = 0,
                                      nclone_range = 3:5,
                                      optim = "optimx",
                                      save_plot = FALSE,
                                      preclustering = "kmedoid")
  ), 1)
  
})

test_that("Check compound, diploid",{
  QC<-QuantumClone(Input_Example,contamination = c(0,0), nclone_range = 3:5,
                   save_plot = FALSE, optim = "compound",
                   Init =1 ,epsilon = 0.01,
                   preclustering = "FLASH",
                   keep.all.model = FALSE,
                   model.selection = 2)
   expect_identical(Compute_NMI(QC),1)
})

test_that("Check compound, triploid",{
  set.seed(121)
  QCat<-QuantumCat(number_of_clones = 2,number_of_mutations = 40,ploidy = "AAB",number_of_samples = 1,depth = 100)
  QC<-QuantumClone(Input_Example,contamination = c(0,0), nclone_range = 3:5,
                   save_plot = FALSE, optim = "compound",
                   Init =1 ,
                   preclustering = "fpc",
                   keep.all.model = FALSE,
                   model.selection = 2)
  expect_identical(Compute_NMI(QC),1)
})

Try the QuantumClone package in your browser

Any scripts or data that you put into this service are public.

QuantumClone documentation built on May 2, 2019, 3:03 a.m.