Nothing
test_that("muts2pp", {
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)
result <- muts2pp(input_data, input_type = "iseq")
result_colnames <- colnames(result)
colnames_len <- length(result_colnames)
expect_that(colnames_len, equals(8))
expect_that(result_colnames[1], equals("gene"))
expect_that(result_colnames[3], equals("chromosome"))
expect_that(result_colnames[6], equals("class"))
expect_that(result_colnames[8], equals("sample"))
})
test_that("fusions2pp", {
demo_file <- system.file("extdata", "demo/proteinpaint/fusions2pp_fusioncatcher.txt",
package = "ngstk")
input_data <- read.table(demo_file, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
disease <- "B-ALL"
sampletype <- "diagnose"
input_data <- data.frame(input_data, disease, sampletype)
input_data$disease <- as.character(input_data$disease)
result <- fusions2pp(input_data, input_type = "fusioncatcher")
result_colnames <- colnames(result)
colnames_len <- length(result_colnames)
expect_that(colnames_len, equals(13))
expect_that(result_colnames[1], equals("disease"))
expect_that(result_colnames[3], equals("gene_a"))
expect_that(result_colnames[6], equals("position_a"))
expect_that(result_colnames[13], equals("patient"))
expect_that(result[1, 3], equals("TCF3"))
expect_that(result[1, 7], equals("PBX1"))
expect_that(result[7, 5], equals("chr4"))
expect_that(result[7, 6], equals("144801564"))
expect_that(result[7, 12], equals("-"))
})
test_that("fusions2pp_meta", {
demo_file <- system.file("extdata", "demo/proteinpaint/fusions2pp_fusioncatcher.txt",
package = "ngstk")
input_data <- read.table(demo_file, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
disease <- "B-ALL"
sampletype <- "diagnose"
input_data <- data.frame(input_data, disease, sampletype)
input_data$disease <- as.character(input_data$disease)
result <- suppressWarnings(fusions2pp_meta(input_data, input_type = "fusioncatcher"))
expect_equal(colnames(result)[1], "sample")
})
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