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

In umccr/gpgr: Genomics Platform Group Reporting

# Generated by roxytest: do not edit by hand!

# File R/purple.R: @testexamples

test_that("Function purple_cnv_som_gene_read() @ L18", {
  
  x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
  (p <- purple_cnv_som_gene_read(x))
  expect_equal(colnames(p)[ncol(p)], "minMinorAlleleCopyNumber")
})


test_that("Function purple_cnv_som_gene_process() @ L62", {
  
  x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
  g <- system.file("extdata/ref/umccr_cancer_genes_2019-03-20.tsv", package = "gpgr")
  (pp <- purple_cnv_som_gene_process(x, g))
  expect_equal(colnames(pp$tab)[ncol(pp$tab)], "minRegSupportStartEndMethod")
})


test_that("Function purple_cnv_som_read() @ L147", {
  
  x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
  (p <- purple_cnv_som_read(x))
  expect_equal(colnames(p)[ncol(p)], "majorAlleleCopyNumber")
})


test_that("Function purple_cnv_som_process() @ L181", {
  
  x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
  (pp <- purple_cnv_som_process(x))
  expect_equal(colnames(pp$tab)[ncol(pp$tab)], "GC (windowCount)")
})


test_that("Function purple_cnv_germ_read() @ L248", {
  
  x <- system.file("extdata/purple/purple.cnv.germline.tsv", package = "gpgr")
  (p <- purple_cnv_germ_read(x))
  expect_equal(colnames(p)[ncol(p)], "majorAlleleCopyNumber")
})


test_that("Function purple_cnv_germ_process() @ L272", {
  
  x <- system.file("extdata/purple/purple.cnv.germline.tsv", package = "gpgr")
  (pp <- purple_cnv_germ_process(x))
  expect_equal(colnames(pp$tab)[ncol(pp$tab)], "GC (windowCount)")
})


test_that("Function purple_version_read() @ L297", {
  
  x <- system.file("extdata/purple/purple.version", package = "gpgr")
  (v <- purple_version_read(x))
  expect_equal(length(v), 2)
  expect_equal(names(v), c("version", "build_date"))
  expect_equal(v$version, "2.51")
})


test_that("Function purple_qc_read() @ L323", {
  
  x <- system.file("extdata/purple/purple.qc", package = "gpgr")
  (q <- purple_qc_read(x))
  expect_true(q$raw[1, "value", drop = TRUE] == "WARN_DELETED_GENES")
})


test_that("Function purple_purity_read() @ L378", {
  
  x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
  (p <- purple_purity_read(x))
  expect_equal(p$raw[1, "column", drop = TRUE], "purity")
  expect_equal(p$raw[nrow(p$raw), "column", drop = TRUE], "svTumorMutationalBurden")
})