| ... | ... |
@@ -14,7 +14,7 @@ expect_equivalent_SE <- function(SE1, SE2) {
|
| 14 | 14 |
assays(SE1) <- endoapply(assays(SE1), as.matrix) |
| 15 | 15 |
assays(SE2) <- endoapply(assays(SE2), as.matrix) |
| 16 | 16 |
if (isTRUE(all.equal(SE1, SE2))) {
|
| 17 |
- return(all.equal(assays(SE1), assays(SE2))) |
|
| 17 |
+ return(invisible(all.equal(assays(SE1), assays(SE2)))) |
|
| 18 | 18 |
} |
| 19 |
- FALSE |
|
| 19 |
+ invisible(FALSE) |
|
| 20 | 20 |
} |
| ... | ... |
@@ -2,19 +2,27 @@ context("BSmooth")
|
| 2 | 2 |
|
| 3 | 3 |
test_that("Errors on bad input", {
|
| 4 | 4 |
expect_error( |
| 5 |
- BSmooth(as(bsseq_test, "SummarizedExperiment")), |
|
| 6 |
- "'BSseq' must be a BSseq object") |
|
| 7 |
- expect_error(BSmooth(rev(bsseq_test)), "'BSseq' must be sorted") |
|
| 5 |
+ object = BSmooth( |
|
| 6 |
+ BSseq = as(bsseq_test, "SummarizedExperiment"), |
|
| 7 |
+ BPPARAM = SerialParam()), |
|
| 8 |
+ regexp = "'BSseq' must be a BSseq object") |
|
| 8 | 9 |
expect_error( |
| 9 |
- BSmooth(resize(bsseq_test, 2)), |
|
| 10 |
- "All loci in 'BSseq' must have width == 1") |
|
| 10 |
+ object = BSmooth(rev(bsseq_test), BPPARAM = SerialParam()), |
|
| 11 |
+ regexp = "'BSseq' must be sorted") |
|
| 12 |
+ expect_error( |
|
| 13 |
+ object = BSmooth(resize(bsseq_test, 2), BPPARAM = SerialParam()), |
|
| 14 |
+ regexp = "All loci in 'BSseq' must have width == 1") |
|
| 11 | 15 |
}) |
| 12 | 16 |
|
| 13 | 17 |
test_that("BSmooth properly inherits 'dir'", {
|
| 14 |
- infile <- system.file("extdata", "test_data.fastq_bismark.bismark.cov.gz",
|
|
| 15 |
- package = "bsseq") |
|
| 16 |
- bsseq <- read.bismark(files = infile, BACKEND = "HDF5Array") |
|
| 17 |
- bsseq <- BSmooth(bsseq) |
|
| 18 |
+ infile <- system.file( |
|
| 19 |
+ "extdata", "test_data.fastq_bismark.bismark.cov.gz", |
|
| 20 |
+ package = "bsseq") |
|
| 21 |
+ bsseq <- read.bismark( |
|
| 22 |
+ files = infile, |
|
| 23 |
+ BACKEND = "HDF5Array", |
|
| 24 |
+ BPPARAM = SerialParam()) |
|
| 25 |
+ bsseq <- BSmooth(bsseq, BPPARAM = SerialParam()) |
|
| 18 | 26 |
expect_is(bsseq, "BSseq") |
| 19 | 27 |
expect_true(hasBeenSmoothed(bsseq)) |
| 20 | 28 |
expect_error( |
| 21 | 29 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,104 @@ |
| 1 |
+context("BSseq-class")
|
|
| 2 |
+ |
|
| 3 |
+test_that("BSseq() allows loci of width != 1", {
|
|
| 4 |
+ bsseq <- BSseq( |
|
| 5 |
+ M = matrix(1:10), |
|
| 6 |
+ Cov = matrix(1:10), |
|
| 7 |
+ gr = GRanges("chr1", IRanges(1:10, width = 10), strand = "*"))
|
|
| 8 |
+ expect_true(validObject(bsseq)) |
|
| 9 |
+}) |
|
| 10 |
+ |
|
| 11 |
+test_that("strandCollapse() does nothing for unstranded data", {
|
|
| 12 |
+ bsseq <- BSseq( |
|
| 13 |
+ M = matrix(1:10), |
|
| 14 |
+ Cov = matrix(1:10), |
|
| 15 |
+ gr = GRanges("chr1", IRanges(1:10, width = 1), strand = "*"))
|
|
| 16 |
+ expect_warning(strandCollapse(bsseq)) |
|
| 17 |
+}) |
|
| 18 |
+ |
|
| 19 |
+test_that("strandCollapse() works on good input", {
|
|
| 20 |
+ nrow <- 20 |
|
| 21 |
+ ncol <- 5 |
|
| 22 |
+ M <- matrix(sample(0:10, size = nrow * ncol, replace = TRUE), ncol = ncol) |
|
| 23 |
+ Cov <- M + sample(0:10, size = nrow * ncol, replace = TRUE) |
|
| 24 |
+ gr_pos <- GRanges( |
|
| 25 |
+ seqnames = c(rep(1, nrow / 2), rep(2, nrow / 2)), |
|
| 26 |
+ ranges = seq(1, 2 * nrow, by = 2), |
|
| 27 |
+ strand = "+") |
|
| 28 |
+ gr_neg <- invertStrand(shift(gr_pos, 1L)) |
|
| 29 |
+ bsseq_pos <- BSseq(M = M, Cov = Cov, gr = gr_pos) |
|
| 30 |
+ bsseq_neg <- BSseq(M = M, Cov = Cov, gr = gr_neg) |
|
| 31 |
+ bsseq <- rbind(bsseq_pos, bsseq_neg) |
|
| 32 |
+ |
|
| 33 |
+ expect_equivalent_SE( |
|
| 34 |
+ SE1 = strandCollapse(bsseq_pos, type = "integer"), |
|
| 35 |
+ SE2 = unstrand(bsseq_pos)) |
|
| 36 |
+ expect_equivalent_SE( |
|
| 37 |
+ SE1 = strandCollapse(bsseq_neg, shift = FALSE, type = "integer"), |
|
| 38 |
+ SE2 = unstrand(bsseq_neg)) |
|
| 39 |
+ expect_equivalent_SE( |
|
| 40 |
+ SE1 = strandCollapse(bsseq_neg, type = "integer"), |
|
| 41 |
+ SE2 = unstrand(shift(bsseq_neg, -1L))) |
|
| 42 |
+ bsseq_strand_collapsed <- strandCollapse(bsseq, type = "integer") |
|
| 43 |
+ expect_identical( |
|
| 44 |
+ object = rowRanges(bsseq_strand_collapsed), |
|
| 45 |
+ expected = unstrand(rowRanges(bsseq_pos))) |
|
| 46 |
+ expect_identical( |
|
| 47 |
+ object = assay(bsseq_strand_collapsed, "M"), |
|
| 48 |
+ expected = assay(bsseq_pos, "M") + assay(bsseq_neg, "M")) |
|
| 49 |
+ expect_identical( |
|
| 50 |
+ object = assay(bsseq_strand_collapsed, "Cov"), |
|
| 51 |
+ expected = assay(bsseq_pos, "Cov") + assay(bsseq_neg, "Cov")) |
|
| 52 |
+ |
|
| 53 |
+ bsseq_strand_collapsed2 <- strandCollapse(bsseq[sample(nrow(bsseq))]) |
|
| 54 |
+ expect_equivalent_SE(bsseq_strand_collapsed, bsseq_strand_collapsed2) |
|
| 55 |
+ |
|
| 56 |
+ bsseq_pos <- realize(bsseq_pos, "HDF5Array") |
|
| 57 |
+ bsseq_neg <- realize(bsseq_neg, "HDF5Array") |
|
| 58 |
+ bsseq <- realize(bsseq, "HDF5Array") |
|
| 59 |
+ expect_equivalent_SE( |
|
| 60 |
+ SE1 = strandCollapse(bsseq_pos, type = "integer"), |
|
| 61 |
+ SE2 = unstrand(bsseq_pos)) |
|
| 62 |
+ expect_equivalent_SE( |
|
| 63 |
+ SE1 = strandCollapse(bsseq_neg, shift = FALSE), |
|
| 64 |
+ SE2 = unstrand(bsseq_neg)) |
|
| 65 |
+ expect_equivalent_SE( |
|
| 66 |
+ SE1 = strandCollapse(bsseq_neg), |
|
| 67 |
+ SE2 = unstrand(shift(bsseq_neg, -1L))) |
|
| 68 |
+ bsseq_strand_collapsed <- strandCollapse(bsseq, type = "integer") |
|
| 69 |
+ expect_identical( |
|
| 70 |
+ object = rowRanges(bsseq_strand_collapsed), |
|
| 71 |
+ expected = unstrand(rowRanges(bsseq_pos))) |
|
| 72 |
+ expect_identical( |
|
| 73 |
+ object = as.matrix(assay(bsseq_strand_collapsed, "M")), |
|
| 74 |
+ expected = as.matrix(assay(bsseq_pos, "M") + assay(bsseq_neg, "M"))) |
|
| 75 |
+ expect_identical( |
|
| 76 |
+ object = as.matrix(assay(bsseq_strand_collapsed, "Cov")), |
|
| 77 |
+ expected = as.matrix(assay(bsseq_pos, "Cov") + assay(bsseq_neg, "Cov"))) |
|
| 78 |
+ |
|
| 79 |
+ bsseq_strand_collapsed2 <- strandCollapse( |
|
| 80 |
+ BSseq = bsseq[sample(nrow(bsseq))], |
|
| 81 |
+ type = "integer") |
|
| 82 |
+ expect_equivalent_SE(bsseq_strand_collapsed, bsseq_strand_collapsed2) |
|
| 83 |
+}) |
|
| 84 |
+ |
|
| 85 |
+test_that("strandCollapse() errors on bad input", {
|
|
| 86 |
+ bsseq <- BSseq( |
|
| 87 |
+ M = matrix(1:3), |
|
| 88 |
+ Cov = matrix(1:3), |
|
| 89 |
+ gr = GRanges( |
|
| 90 |
+ seqnames = "chr1", |
|
| 91 |
+ ranges = IRanges(1:3, width = 1), |
|
| 92 |
+ strand = c("+", "-", "*")))
|
|
| 93 |
+ expect_error(strandCollapse(bsseq)) |
|
| 94 |
+}) |
|
| 95 |
+ |
|
| 96 |
+test_that("strandCollapse() will unstrand loci and may re-order them", {
|
|
| 97 |
+ bsseq <- BSseq( |
|
| 98 |
+ M = matrix(1:10), |
|
| 99 |
+ Cov = matrix(1:10), |
|
| 100 |
+ gr = GRanges("chr1", IRanges(10:1, width = 1), strand = "+"))
|
|
| 101 |
+ expect_true(all(strand(strandCollapse(bsseq)) == "*")) |
|
| 102 |
+ expect_false(expect_equivalent_SE(strandCollapse(bsseq), bsseq)) |
|
| 103 |
+ expect_equivalent_SE(strandCollapse(bsseq), bsseq[10:1]) |
|
| 104 |
+}) |
