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# This tests that various functions are applicable with alternative matrix representations.
# library(scran); library(testthat); source("test-altrep.R")
set.seed(99999)
library(Matrix)
X <- as(matrix(rpois(100000, lambda=1), ncol=100), "dgCMatrix")
X_ <- as.matrix(X)
library(HDF5Array)
Y <- as(matrix(rpois(100000, lambda=5), ncol=100), "HDF5Array")
Y_ <- as.matrix(Y)
test_that("cyclone runs properly", {
mm.pairs <- readRDS(system.file("exdata", "mouse_cycle_markers.rds", package="scran"))
rownames(X) <- rownames(X_) <- sample(mm.pairs$G1[,1], nrow(X))
rownames(Y) <- rownames(Y_) <- sample(mm.pairs$G1[,1], nrow(Y))
set.seed(100)
assignments1 <- cyclone(X[,1:10], mm.pairs)
set.seed(100)
assignments2 <- cyclone(X_[,1:10], mm.pairs)
expect_identical(assignments1, assignments2)
set.seed(100)
assignments1 <- cyclone(Y[,1:10], mm.pairs)
set.seed(100)
assignments2 <- cyclone(Y_[,1:10], mm.pairs)
expect_identical(assignments1, assignments2)
})
test_that("Variance estimation runs properly", {
dec1 <- modelGeneVar(Y)
dec2 <- modelGeneVar(Y_)
expect_equal(dec1, dec2)
dec1 <- modelGeneCV2(Y)
dec2 <- modelGeneCV2(Y_)
expect_equal(dec1, dec2)
})
test_that("correlatePairs runs properly", {
set.seed(1000)
null <- correlateNull(ncol(X), iters=1e6)
set.seed(100)
ref <- correlatePairs(X_[1:10,], null.dist=null)
set.seed(100)
alt <- correlatePairs(X[1:10,], null.dist=null)
expect_equal(ref, alt)
set.seed(200)
ref <- correlatePairs(Y_[20:50,], null.dist=null)
set.seed(200)
alt <- correlatePairs(Y[20:50,], null.dist=null)
expect_equal(ref, alt)
})
test_that("buildSNNGraph with irlba runs properly on sparse matrices", {
set.seed(1000)
g1 <- buildSNNGraph(X, BSPARAM=BiocSingular::IrlbaParam())
set.seed(1000)
g2 <- buildSNNGraph(X_, BSPARAM=BiocSingular::IrlbaParam())
expect_identical(g1[], g2[])
set.seed(100)
g1 <- buildSNNGraph(X, d=10, BSPARAM=BiocSingular::IrlbaParam())
set.seed(100)
g2 <- buildSNNGraph(X_, d=10, BSPARAM=BiocSingular::IrlbaParam())
expect_identical(g1[], g2[])
})
test_that("findMarkers and overlapExprs work properly", {
groups <- sample(2, ncol(X), replace=TRUE)
expect_equal(findMarkers(Y, groups), findMarkers(Y_, groups))
})
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