tests/testthat/test-roxytest-tests-sig_tally.R

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

# Generated by roxytest: do not edit by hand!

# File R/sig_tally.R: @tests

test_that("Function sig_tally() @ L114", {
  ## Load copy number object
  load(system.file("extdata", "toy_copynumber.RData",
    package = "sigminer", mustWork = TRUE
  ))
  # Use method designed by Wang, Shixiang et al.
  cn_tally_W <- sig_tally(cn, method = "W")
  # Use method designed by Tao & Wang.
  cn_tally_T <- sig_tally(cn, method = "T")
  
  expect_equal(length(cn_tally_T), 5L)
  
  ## for SBS
  
  laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
  laml <- read_maf(maf = laml.maf)
  if (require("BSgenome.Hsapiens.UCSC.hg19")) {
    mt_tally <- sig_tally(
      laml,
      ref_genome = "BSgenome.Hsapiens.UCSC.hg19",
      use_syn = TRUE
    )
  
    expect_equal(length(mt_tally), 3L)
  
    ## Use strand bias categories
    mt_tally <- sig_tally(
      laml,
      ref_genome = "BSgenome.Hsapiens.UCSC.hg19",
      use_syn = TRUE, add_trans_bias = TRUE
    )
    ## Test it by enrichment analysis
    dt1 = enrich_component_strand_bias(mt_tally$nmf_matrix)
    dt2 = enrich_component_strand_bias(mt_tally$all_matrices$SBS_24)
  
    expect_s3_class(dt1, "data.table")
    expect_s3_class(dt2, "data.table")
  } else {
    message("Please install package 'BSgenome.Hsapiens.UCSC.hg19' firstly!")
  }
})