tests/testthat/test_count_per_gene.R

In cbaumbach/genFun: Functions For Dealing With Genetic Data

context("count_per_gene")

# Notation used in test cases:
#     points:  chr|pos
#     genes:   chr[start,end]

f <- count_per_gene

test_that("gene_start, gene_end, and gene_chr must be of the same length", {
    msg <- "gene_start, gene_end, and gene_chr must be of the same length"
    expect_error(f(0, 0, 0, 0:1, 0:1), msg)
})

test_that("pos and chr must be of the same length", {
    msg <- "pos and chr must be of the same length"
    expect_error(f(0, 0:1, 0, 0, 0), msg)
})

test_that("0|0 -> 0[0,0] -> 1", expect_equal(f(0, 0, 0, 0, 0), 1))
test_that("0|0 -> 0[1,1] -> 0", expect_equal(f(0, 0, 1, 1, 0), 0))
test_that("0|0 -> 0[NA,0] -> NA", expect_equal(f(0, 0, NA, 0, 0), NA_integer_))
test_that("0|0 -> 0[0,NA] -> NA", expect_equal(f(0, 0, 0, NA, 0), NA_integer_))
test_that("0|0 -> 0[NA,NA] -> NA", expect_equal(f(0, 0, NA, NA, 0), NA_integer_))
test_that("0|0 -> 1[0,0] -> 0", expect_equal(f(0, 0, 0, 0, 1), 0))
test_that("0|0 -> 0['0',0] -> 1", expect_equal(f(0, 0, "0", 0, 0), 1))
test_that("0|0 -> 0[0,'0'] -> 1", expect_equal(f(0, 0, 0, "0", 0), 1))
test_that("0|0 -> 0['0','0'] -> 1", expect_equal(f(0, 0, "0", "0", 0), 1))
test_that("0|'0' -> 0[0,0] -> 1", expect_equal(f("0", 0, 0, 0, 0), 1))
test_that("0|0 -> 'foo'[0,0] -> 0", expect_equal(f(0, 0, 0, 0, "foo"), 0))

test_that("0|0 -> 0[0,0] 0[1,1] 0[0,0] -> 1 0 1", {
    expect_equal(f(0, 0, c(0,1,0), c(0,1,0), c(0,0,0)), c(1,0,1))
})

test_that("0|0 1|0 -> 1[0,0] 0[0,0] 1[1,1] 0[1,1] 1[0,0] 0[0,0] -> 1 1 0 0 1 1", {
    expect_equal(f(pos = c(0,0),
                   chr = c(0,1),
                   gene_start = c(0,0,1,1,0,0),
                   gene_end   = c(0,0,1,1,0,0),
                   gene_chr   = c(1,0,1,0,1,0)),
        c(1,1,0,0,1,1))
})

test_that("NULL|NULL -> 0[0,0] -> 0", {
    expect_equal(f(NULL, NULL, 0, 0, 0), 0)
})

test_that("0|0 -> NULL[NULL,NULL] -> empty", {
    expect_equal(f(0, 0, NULL, NULL, NULL), integer())
})

test_that("NULL|NULL -> NULL[NULL,NULL] -> empty", {
    expect_equal(f(NULL, NULL, NULL, NULL, NULL), integer())
})

test_that("empty|empty -> 0[0,0] -> 0", {
    expect_equal(f(integer(), integer(), 0, 0, 0), 0)
})

test_that("0|0 -> empty[empty,empty] -> empty", {
    expect_equal(f(0, 0, integer(), integer(), integer()), integer())
})

test_that("empty|empty -> empty[empty,empty] -> empty", {
    expect_equal(f(integer(), integer(), integer(), integer(), integer()), integer())
})

test_that("chromosomes don't need to be ordered", {
    intervals <- utils::read.table(text = "
# chromosomes 1-3, intervals: [0,10], [20,30], [40,50]
chr  start  end
1     0     10
2    20     30
1    40     50
3     0     10
1    20     30
3    40     50
2     0     10
3    20     30
2    40     50
", header = TRUE, stringsAsFactor = FALSE)
    points_on_one_chr <- seq(0L, 50L, 5L)
    points <- data.frame(pos = rep(points_on_one_chr, each = 3L), chr = 1:3)
    points_per_interval <- 3L
    intervals$expected <- points_per_interval
    intervals$actual <- f(points$pos, points$chr,
        intervals$start, intervals$end, intervals$chr)
    expect_equal(intervals$actual, intervals$expected)
})