tests/testthat/test-tabToDNVcatalogue.R

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

context("testing conversion from dataframe of SNV to DNV catalogue")

test_that("test tabToDNVcatalogue() to convert a tab file with SNV into an DNV catalogue.", {
  
  testSNVdf <- read.table(file = "test_DNVs.snv.simple.txt",
                          sep = "\t",header = TRUE,check.names = FALSE,stringsAsFactors = FALSE)
  testSNVdf <- testSNVdf[,c("Chrom","Pos","Ref","Alt")]
  colnames(testSNVdf) <- c("chr","position","REF","ALT")
  
  expected_cat <- read.table(file="test.dnv.expected.tab",sep = "\t",header = TRUE,stringsAsFactors = FALSE)
  
  res_cat <- tabToDNVcatalogue(testSNVdf)
  obtained_cat <- res_cat$DNV_catalogue
  colnames(obtained_cat) <- "sample1"
  
  expect_equal(obtained_cat,expected_cat)
  
})