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# Tests the convertTo function.
# require(scran); require(testthat); source("test-convert.R")
set.seed(40000)
ncells <- 200
ngenes <- 1000
count.sizes <- rnbinom(ncells, mu=100, size=5)
dummy <- matrix(count.sizes, ncol=ncells, nrow=ngenes, byrow=TRUE)
rownames(dummy) <- paste0("X", seq_len(ngenes))
colnames(dummy) <- paste0("Y", seq_len(ncells))
X <- SingleCellExperiment(list(counts=dummy))
sizeFactors(X) <- 2^rnorm(ncells)
rowData(X)$SYMBOL <- paste0("X", seq_len(ngenes))
X$other <- sample(LETTERS, ncells, replace=TRUE)
# Converting to a DGEList.
test_that("Can convert from SingleCellExperiment to DGEList", {
y <- convertTo(X, type="edgeR")
expect_identical(y$counts, counts(X))
# Checking subsetting behaves as expected.
chosen <- c(50:1, 101:200)
y <- convertTo(X, type="edgeR", subset.row=chosen)
expect_identical(y$counts, counts(X)[chosen,])
# Checking metadata behaves as expected.
y <- convertTo(X, type="edgeR")
expect_identical(y$samples$other, X$other)
expect_identical(y$genes$SYMBOL, rowData(X)$SYMBOL)
# Trying out silly settings.
expect_warning(y <- convertTo(X[0,], type="edgeR"))
expect_identical(y$counts, counts(X)[0,])
expect_identical(y$genes$SYMBOL, character(0))
y <- convertTo(X[,0], type="edgeR")
expect_identical(y$counts, counts(X)[,0])
expect_identical(y$samples$other, character(0))
})
test_that("Can convert SingleCellExperiment to a DESeqDataSet", {
library(DESeq2)
y <- convertTo(X, type="DESeq2")
expect_equal(counts(y), counts(X))
expect_identical(unname(sizeFactors(y)), sizeFactors(X))
# Checking subsetting behaves as expected.
chosen <- c(50:1, 101:200)
y <- convertTo(X, type="DESeq2", subset.row=chosen)
expect_equivalent(assay(y), counts(X)[chosen,])
# Checking metadata is extracted as expected.
y <- convertTo(X, type="DESeq2")
expect_identical(y$other, X$other)
expect_identical(mcols(y)$SYMBOL, rowData(X)$SYMBOL)
})
# Converting to a CellDataSet.
catch_warning <- function(...) {
expect_warning(..., "gene_short_name")
}
get_exprs <- function(y) {
assayDataElement(y, "exprs")
}
test_that("Can convert SingleCellExperiment to a CellDataSet", {
skip("monocle is a little broken because of clusterApply")
catch_warning(y <- convertTo(X, type="monocle"))
expect_equal(get_exprs(y), counts(X))
expect_equivalent(sizeFactors(y), sizeFactors(X))
# Checking that subsetting works as expected.
chosen <- c(50:1, 101:200)
catch_warning(y <- convertTo(X, type="monocle", subset.row=chosen))
expect_equal(get_exprs(y), counts(X)[chosen,])
expect_equivalent(sizeFactors(y), sizeFactors(X))
# Checking metadata is extracted as expected.
catch_warning(y <- convertTo(X, type="monocle"))
expect_identical(y$other, X$other)
expect_identical(fData(y)$SYMBOL, rowData(X)$SYMBOL)
# # Looks like the CellDataSet constructor just fails with no rows.
# y <- convertTo(X[0,], type="monocle", row.fields="SYMBOL")
# expect_identical(get_exprs(y), counts(X)[0,])
# expect_identical(fData(y)$SYMBOL, character(0))
catch_warning(y <- convertTo(X[,0], type="monocle") )
expect_identical(get_exprs(y), counts(X)[,0])
expect_identical(y$other, character(0))
X2 <- X
sizeFactors(X2) <- NULL
expect_warning(y2 <- convertTo(X2, type="monocle"))
expect_equal(counts(X2), get_exprs(y2))
expect_true(all(is.na(sizeFactors(y2))))
})
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