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# Tests for size factor calculations.
# library(scuttle); library(testthat); source("setup.R"); source("test-size-factors.R")
X <- sce
dummy <- counts(X)
test_that("librarySizeFactors works as expected", {
sf <- librarySizeFactors(X)
expect_identical(mean(sf), 1)
expect_true(sd(sf/colSums(dummy)) < 1e-8)
X <- computeLibraryFactors(X)
expect_identical(sf, sizeFactors(X))
sf <- librarySizeFactors(X, subset.row=1:10)
expect_identical(mean(sf), 1)
expect_true(sd(sf/colSums(dummy[1:10,])) < 1e-8)
})
test_that("geometric size factors work as expected", {
sf <- geometricSizeFactors(X)
expect_equal(mean(sf), 1)
expect_true(sd(sf/exp(colMeans(log1p(dummy)))) < 1e-8)
X <- computeGeometricFactors(X)
expect_identical(sf, sizeFactors(X))
sf <- geometricSizeFactors(X, subset.row=100:200)
expect_identical(mean(sf), 1)
expect_true(sd(sf/exp(colMeans(log1p(dummy[100:200,])))) < 1e-8)
})
test_that("medianSizeFactors works as expected", {
sf <- medianSizeFactors(X)
expect_equal(mean(sf), 1)
X <- computeMedianFactors(X)
expect_identical(sf, sizeFactors(X))
sf <- medianSizeFactors(X, subset.row=1:10)
expect_equal(mean(sf), 1)
expect_identical(sf, medianSizeFactors(X[1:10,]))
ref <- runif(nrow(X))
sf <- medianSizeFactors(X, subset.row=100:200, reference=ref)
expect_identical(mean(sf), 1)
expect_identical(sf, medianSizeFactors(X[100:200,], reference=ref[100:200]))
# Same results if we whack on a bunch of zeroes.
ref <- medianSizeFactors(dummy)
sf2 <- medianSizeFactors(rbind(0, dummy))
expect_equal(ref, sf2)
ref <- medianSizeFactors(dummy, subset.row=1:10)
sf2 <- medianSizeFactors(rbind(0, dummy), subset.row=2:11)
expect_equal(ref, sf2)
})
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