tests/testthat/test-SignatureFit.R

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

context("testing Signature Fit, should take a few seconds")

test_that("test that SignatureFit_withBootstrap() works on a random matrix, will take a few minutes ", {
  #test substitutions
  mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
  n_row <- 96
  n_col <- 15
  rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
  colnames(rnd_matrix) <- paste0("C",1:n_col)
  row.names(rnd_matrix) <- mut.order
  res <- SignatureFit_withBootstrap(cat = rnd_matrix,
                                    signature_data_matrix = cosmic30,
                                    nboot = 5,
                                    threshold_percent = 0.1,
                                    threshold_p.value = 0.1)

  #here goes the test
  expect_true(TRUE)
})

test_that("test that SignatureFit_withBootstrap() works on a random matrix, and that random seed works, no parallel ", {
  #test substitutions
  mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
  n_row <- 96
  n_col <- 5
  rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
  colnames(rnd_matrix) <- paste0("C",1:n_col)
  row.names(rnd_matrix) <- mut.order
  res1 <- SignatureFit_withBootstrap(cat = rnd_matrix,
                                    signature_data_matrix = cosmic30,
                                    nboot = 5,
                                    threshold_percent = 0,
                                    threshold_p.value = 0.1,
                                    nparallel = 1,
                                    randomSeed = 1)
  res2 <- SignatureFit_withBootstrap(cat = rnd_matrix,
                                     signature_data_matrix = cosmic30,
                                     nboot = 5,
                                     threshold_percent = 0,
                                     threshold_p.value = 0.1,
                                     nparallel = 1,
                                     randomSeed = 1)
  
  #here goes the test
  expect_equal(res1$E_median_filtered,res2$E_median_filtered)
})

test_that("test that SignatureFit_withBootstrap() works on a random matrix, and that random seed works, using parallel ", {
  #test substitutions
  mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
  n_row <- 96
  n_col <- 5
  rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
  colnames(rnd_matrix) <- paste0("C",1:n_col)
  row.names(rnd_matrix) <- mut.order
  res1 <- SignatureFit_withBootstrap(cat = rnd_matrix,
                                     signature_data_matrix = cosmic30,
                                     nboot = 5,
                                     threshold_percent = 0,
                                     threshold_p.value = 0.1,
                                     nparallel = 2,
                                     randomSeed = 1)
  res2 <- SignatureFit_withBootstrap(cat = rnd_matrix,
                                     signature_data_matrix = cosmic30,
                                     nboot = 5,
                                     threshold_percent = 0,
                                     threshold_p.value = 0.1,
                                     nparallel = 2,
                                     randomSeed = 1)
  
  #here goes the test
  expect_equal(res1$E_median_filtered,res2$E_median_filtered)
})

test_that("test that SignatureFit_withBootstrap_Analysis() works on a random matrix, will take a few minutes ", {
  #test substitutions
  mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
  n_row <- 96
  n_col <- 15
  rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
  colnames(rnd_matrix) <- paste0("C",1:n_col)
  row.names(rnd_matrix) <- mut.order
  res <- SignatureFit_withBootstrap_Analysis(outdir = "test_fit/",
                                             cat = rnd_matrix,
                                             signature_data_matrix = cosmic30,
                                             nboot = 5,
                                             threshold_percent = 0.1,
                                             threshold_p.value = 0.1)
  
  unlink("test_fit/", recursive = TRUE)
  
  #here goes the test
  expect_true(TRUE)
})

test_that("test that SignatureFit_withBootstrap() works on a random matrix, and then plots, will take a few minutes ", {
  #test substitutions
  mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
  n_row <- 96
  n_col <- 15
  rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
  colnames(rnd_matrix) <- paste0("C",1:n_col)
  row.names(rnd_matrix) <- mut.order
  res <- SignatureFit_withBootstrap(cat = rnd_matrix,
                                    signature_data_matrix = cosmic30,
                                    nboot = 5,
                                    threshold_percent = 0.1,
                                    threshold_p.value = 0.1)
  
  plot_SignatureFit_withBootstrap(outdir = "test_fit/",boostrapFit_res = res,type_of_mutations = "subs")
  
  unlink("test_fit/", recursive = TRUE)
  
  #here goes the test
  expect_true(TRUE)
})