tests/testthat/test_CombP.R

In GenRank: Candidate gene prioritization based on convergent evidence

context("CombP")

test_that("Output of CombP is correct", {
    input_file_P <- system.file("extdata","CombP_toydata.txt",package="GenRank")
    CP_ranking <- CombP(input_file_P, method = "fisher", na.remove = TRUE)
    expect_that(is.data.frame(CP_ranking), is_true())
    expect_that(ncol(CP_ranking), equals(3))
    expect_that(is.factor(CP_ranking[, 1]), is_true())
    expect_that(is.numeric(CP_ranking[, 2]), is_true())
    expect_that(is.integer(CP_ranking[, 3]), is_true())
    expect_that(is.unsorted(CP_ranking[, 2]), is_false())
    expect_that(is.unsorted(CP_ranking[, 3]), is_false())
})

test_that("CombP stops if wrong input", {
    input_file_P <- system.file("extdata","CombP_toydata.txt",package="GenRank")
    input_dat <- read.table(input_file_P,header=F, sep='\t',stringsAsFactors = FALSE)
    expect_that(ncol(input_dat)>2, is_true())
    expect_that(is.character(input_dat[, 1]), is_true())
    expect_that(is.numeric(input_dat[, 3]), is_true())
    expect_error(CombP(input_file_P), "need.*")
    expect_error(CombP(input_file_P, "fisher"), "need.*")
    expect_error(CombP(input_file_P, method = "fisher"), "NAs.*")
    expect_error(CombP(input_file_P, method = "Fisher"), "method.*")
})