tests/testthat/test_f_cbioportal_transefer.R

In JhuangLab/ngstk: Next-Generation Sequencing (NGS) Data Analysis Toolkit

test_that("muts2mutation_mapper", {
  demo_file <- system.file("extdata", "demo/proteinpaint/muts2pp_iseq.txt", package = "ngstk")
  input_data <- read.table(demo_file, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
  disease <- "T-ALL"
  input_data <- data.frame(input_data, disease)
  input_data$disease <- as.character(input_data$disease)
  suppressWarnings(result <- muts2mutation_mapper(input_data, input_type = "iseq"))
  result_colnames <- colnames(result)
  colnames_len <- length(result_colnames)
  expect_that(colnames_len, equals(12))
  expect_that(result_colnames[1], equals("Hugo_Symbol"))
  expect_that(result_colnames[3], equals("Protein_Change"))
  expect_that(result_colnames[6], equals("Start_Position"))
  expect_that(result_colnames[8], equals("Reference_Allele"))
})

test_that("muts2oncoprinter", {
  demo_file <- system.file("extdata", "demo/proteinpaint/muts2pp_iseq.txt", package = "ngstk")
  input_data <- read.table(demo_file, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
  disease <- "T-ALL"
  input_data <- data.frame(input_data, disease)
  input_data$disease <- as.character(input_data$disease)
  suppressWarnings(result <- muts2oncoprinter(input_data, input_type = "iseq"))
  result_colnames <- colnames(result)
  colnames_len <- length(result_colnames)
  expect_that(colnames_len, equals(4))
  expect_that(result_colnames[1], equals("Sample"))
  expect_that(result_colnames[2], equals("Gene"))
  expect_that(result_colnames[3], equals("Alteration"))
  expect_that(result_colnames[4], equals("Type"))
})

test_that("fusions2oncoprinter", {
  demo_file <- system.file("extdata", "demo/proteinpaint/fusions2pp_fusioncatcher.txt", 
    package = "ngstk")
  input_data <- read.table(demo_file, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
  suppressWarnings(result <- fusions2oncoprinter(input_data, input_type = "fusioncatcher"))
  result_colnames <- colnames(result)
  colnames_len <- length(result_colnames)
  expect_that(colnames_len, equals(5))
  expect_that(result_colnames[1], equals("Sample"))
  expect_that(result_colnames[2], equals("Gene_a"))
  expect_that(result_colnames[3], equals("Gene_b"))
  expect_that(result_colnames[4], equals("Alteration"))
  expect_that(result_colnames[5], equals("Type"))
})