Nothing
# Get matrices for each batch.
m1 <- SimBatches$batches[[1]]
m2 <- SimBatches$batches[[2]]
# Fix column (cells) names.
colnames(m1) <- paste0("B1_", colnames(m1))
colnames(m2) <- paste0("B2_", colnames(m2))
# Initialize batch information.
b1 <- rep("B1", ncol(m1))
b2 <- rep("B2", ncol(m2))
# Combine batches.
b <- c(b1, b2)
m <- cbind(m1, m2)
cellnames <- colnames(m)
# Create Seurat object.
x <- Seurat::CreateSeuratObject(Seurat::as.sparse(m))
x$batch <- b
# Create SingleCellExperiment object.
y <- SingleCellExperiment::SingleCellExperiment(list(counts=m, logcounts=m))
y$batch <- b
# RunCanek.
x <- RunCanek(x, "batch", slot="counts")
y <- RunCanek(y, "batch")
z <- RunCanek(list(B1=m1, B2=m2), debug = TRUE)
test_that("RunCanek works on Seurat objects", {
expect_false(is.null(x))
expect_is(x, "Seurat")
expect_length(Seurat::Assays(x), 2)
expect_equal(Seurat::Assays(x), c("RNA", "Canek"))
expect_equal(colnames(x), cellnames)
})
test_that("RunCanek works on SingleCellExperiment objects", {
expect_false(is.null(y))
expect_is(y, "SingleCellExperiment")
expect_length(SummarizedExperiment::assays(y), 3)
expect_equal(names(SummarizedExperiment::assays(y)), c("counts", "logcounts", "Canek"))
expect_equal(colnames(y), cellnames)
})
test_that("RunCanek works on lists", {
expect_false(is.null(z))
expect_is(z, "list")
expect_length(z, 3)
expect_equal(names(z), c("B2/B1", "Batches Integrated", "Total_Correction_Time"))
expect_equal(colnames(z$`Batches Integrated`), cellnames)
expect_error(CorrectBatches(list(B1 = SimBatches$batches$B1, B2 = SimBatches$batches$B1)))
})
x <- RunCanek(x, "batch", integration.name = "CanekRNA")
y <- RunCanek(y, "batch", integration.name = "CanekRNA")
test_that("Setting RunCanek integration.name argument works", {
expect_true("CanekRNA" %in% names(x))
expect_true("CanekRNA" %in% names(SummarizedExperiment::assays(y)))
})
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