1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
|
# This tests the cleanSizeFactors() function.
# library(scuttle); library(testthat); source("test-clean-size-factors.R")
set.seed(1000)
test_that("cleanSizeFactors works correctly", {
N <- 100
sf <- runif(N)
num <- jitter(sf/(sf+1)) # nls() fails on zero-residual data.
# Does nothing; just returns the size factors directly.
out <- cleanSizeFactors(sf, num)
expect_equal(sf, out)
# Fills in the expected values.
expect_warning(out <- cleanSizeFactors(c(-sf, sf), c(num, num)))
expect_identical(sf, tail(out, N))
expect_equal(sf, head(out, N), tol=1e-3)
# Handles cases where the number of genes is greater than possible.
expect_warning(out <- cleanSizeFactors(c(-1, sf), c(2, num)))
expect_equal(out[1], max(sf))
# Avoids warnings when there is actually a decent amount of noise.
jnum <- num * 2^rnorm(N, sd=0.1)
expect_warning(out <- cleanSizeFactors(c(-1, sf), c(0.5, jnum)), NA)
expect_identical(sf, tail(out, -1))
})
set.seed(1001)
test_that("robustness iterations make a difference in cleanSizeFactors", {
N <- 100
sf <- runif(N)
num <- jitter(sf/(sf+1))
sf2 <- c(sf, 0.1, -sf) # adding an outlier.
num2 <- c(num, 1, num)
expect_warning(out <- cleanSizeFactors(sf2, num2))
expect_identical(sf, head(out, N))
expect_equal(sf, tail(out, N), tol=1e-3)
# Without robustness, it does not return accurate values.
out <- cleanSizeFactors(sf2, num2, iterations=0)
expect_identical(sf, head(out, N))
expect_false(all(abs(tail(out, N) - sf) < 1e-3))
})
set.seed(1002)
test_that("cleanSizeFactors behaves in a live example", {
counts <- matrix(rpois(20000, lambda=runif(100)), ncol=100, byrow=TRUE)
# Adding negative values:
num <- c(100, colSums(counts>0))
sf <- c(-1, colSums(counts))
out <- cleanSizeFactors(sf, num)
expect_identical(tail(sf, -1), tail(out, -1))
expect_true(out[1] > mean(sf[num < 100]))
expect_true(out[1] < mean(sf[num > 100]))
})
test_that("cleanSizeFactors avoids silly inputs", {
expect_identical(cleanSizeFactors(numeric(0), integer(0)), numeric(0))
expect_error(cleanSizeFactors(-1, integer(0)), "same length")
expect_error(cleanSizeFactors(-(1:10), 1:10), "need at least")
})
|
