tests/testthat/test-roxytest-testexamples-sig_fit_bootstrap.R

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

# Generated by roxytest: do not edit by hand!

# File R/sig_fit_bootstrap.R: @testexamples

test_that("Function sig_fit_bootstrap() @ L61", {
  
  W <- matrix(c(1, 2, 3, 4, 5, 6), ncol = 2)
  colnames(W) <- c("sig1", "sig2")
  W <- apply(W, 2, function(x) x / sum(x))
  
  H <- matrix(c(2, 5, 3, 6, 1, 9, 1, 2), ncol = 4)
  colnames(H) <- paste0("samp", 1:4)
  
  V <- W %*% H
  V
  
  if (requireNamespace("quadprog", quietly = TRUE)) {
    H_bootstrap <- sig_fit_bootstrap(V[, 1], W, n = 10, type = "absolute")
    ## Typically, you have to run many times to get close to the answer
    boxplot(t(H_bootstrap$expo))
    H[, 1]
  
    ## Return P values
    ## In practice, run times >= 100
    ## is recommended
    report_bootstrap_p_value(H_bootstrap)
    ## For multiple samples
    ## Input a list
    report_bootstrap_p_value(list(samp1 = H_bootstrap, samp2 = H_bootstrap))
  
    #   ## Find suboptimal decomposition
    #   H_suboptimal <- sig_fit_bootstrap(V[, 1], W,
    #     n = 10,
    #     type = "absolute",
    #     method = "SA",
    #     find_suboptimal = TRUE
    #   )
  }
  expect_is(H_bootstrap, "list")
})