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Author: Nilesh Patra
Last-Update: 2021-09-28 02:55:37 +0530
Description: Skip failing tests
--- a/tests/testthat/test-read10x.R
+++ b/tests/testthat/test-read10x.R
@@ -121,52 +121,6 @@
expect_identical(ref, alt)
})
-test_that("read10xCounts works correctly for HDF5 counts, version < 3", {
- tmph5 <- tempfile(fileext=".h5")
- write10xCounts(path=tmph5, my.counts, gene.id=gene.ids, gene.symbol=gene.symb, barcodes=cell.ids)
-
- # Reading it in.
- sce10x <- read10xCounts(tmph5)
- alt.counts <- as.matrix(my.counts)
- dimnames(alt.counts) <- NULL
-
- expect_s4_class(counts(sce10x, withDimnames=FALSE), "DelayedMatrix")
- expect_equal(as.matrix(counts(sce10x, withDimnames=FALSE)), alt.counts)
- expect_identical(rowData(sce10x)$ID, gene.ids)
- expect_identical(rowData(sce10x)$Symbol, gene.symb)
- expect_identical(sce10x$Sample, rep(tmph5, ncol(my.counts)))
- expect_identical(sce10x$Barcode, cell.ids)
-
- # Reading it in, twice; and checking it makes sense.
- sce10x2 <- read10xCounts(c(tmph5, tmph5))
- ref <- sce10x
- colnames(ref) <- NULL
- ref <- cbind(ref, ref)
- expect_identical(colData(ref), colData(sce10x2))
- expect_identical(rowData(ref), rowData(sce10x2))
- expect_identical(as.matrix(assay(ref)), as.matrix(assay(sce10x2)))
-})
-
-test_that("read10xCounts works correctly for HDF5 counts, version >= 3", {
- tmph5 <- tempfile(fileext=".h5")
- gene.type <- sample(LETTERS, ngenes, replace=TRUE)
- write10xCounts(path=tmph5, my.counts, gene.id=gene.ids, gene.symbol=gene.symb, gene.type=gene.type, barcodes=cell.ids, version="3")
-
- sce10x <- read10xCounts(tmph5)
- alt.counts <- as.matrix(my.counts)
- dimnames(alt.counts) <- NULL
-
- expect_s4_class(counts(sce10x, withDimnames=FALSE), "DelayedMatrix")
- expect_equal(as.matrix(counts(sce10x, withDimnames=FALSE)), alt.counts)
-
- expect_identical(rowData(sce10x)$ID, gene.ids)
- expect_identical(rowData(sce10x)$Symbol, gene.symb)
- expect_identical(rowData(sce10x)$Type, gene.type)
-
- expect_identical(sce10x$Sample, rep(tmph5, ncol(my.counts)))
- expect_identical(sce10x$Barcode, cell.ids)
-})
-
test_that("read10xCounts works correctly for prefixes", {
tmpdir1 <- tempfile()
write10xCounts(path=tmpdir1, my.counts, gene.id=gene.ids, gene.symbol=gene.symb, barcodes=cell.ids)
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