| 352 | 351 |
deleted file mode 100644 |
| ... | ... |
@@ -1,66 +0,0 @@ |
| 1 |
-test_read.bismark_coverage <- function() {
|
|
| 2 |
- # Test that read.bismark() works on good input |
|
| 3 |
- infile <- system.file("extdata", "test_data.fastq_bismark.bismark.cov.gz",
|
|
| 4 |
- package = "bsseq") |
|
| 5 |
- bsseq <- read.bismark(files = infile, |
|
| 6 |
- sampleNames = "test_data", |
|
| 7 |
- rmZeroCov = FALSE, |
|
| 8 |
- strandCollapse = FALSE, |
|
| 9 |
- fileType = "cov", |
|
| 10 |
- verbose = FALSE) |
|
| 11 |
- checkTrue(is(bsseq, "BSseq")) |
|
| 12 |
- # Regression check |
|
| 13 |
- # Should not fail if sampleNames have names() |
|
| 14 |
- bsseq <- read.bismark(files = infile, |
|
| 15 |
- sampleNames = c(test = "test_data"), |
|
| 16 |
- rmZeroCov = FALSE, |
|
| 17 |
- strandCollapse = FALSE, |
|
| 18 |
- fileType = "cov", |
|
| 19 |
- verbose = FALSE) |
|
| 20 |
- checkTrue(is(bsseq, "BSseq")) |
|
| 21 |
- |
|
| 22 |
- # Should also work because the "cov" fileType is the same as the |
|
| 23 |
- # "oldBedGraph" fileType |
|
| 24 |
- bsseq <- read.bismark(files = infile, |
|
| 25 |
- sampleNames = "test_data", |
|
| 26 |
- rmZeroCov = FALSE, |
|
| 27 |
- strandCollapse = FALSE, |
|
| 28 |
- fileType = "oldBedGraph", |
|
| 29 |
- verbose = FALSE) |
|
| 30 |
- checkTrue(is(bsseq, "BSseq")) |
|
| 31 |
- |
|
| 32 |
- # Test that read.bismark() fails if given incorrect fileType. |
|
| 33 |
- checkException(read.bismark(files = infile, |
|
| 34 |
- sampleNames = "test_data", |
|
| 35 |
- rmZeroCov = FALSE, |
|
| 36 |
- strandCollapse = FALSE, |
|
| 37 |
- fileType = "cytosineReport", |
|
| 38 |
- verbose = FALSE)) |
|
| 39 |
-} |
|
| 40 |
- |
|
| 41 |
-test_read.bismark_cytosineReport <- function() {
|
|
| 42 |
- # Test that read.bismark() works on good input |
|
| 43 |
- infile <- system.file("extdata", "test_data.cytosineReport.gz",
|
|
| 44 |
- package = "bsseq") |
|
| 45 |
- bsseq <- read.bismark(files = infile, |
|
| 46 |
- sampleNames = "test_data", |
|
| 47 |
- rmZeroCov = FALSE, |
|
| 48 |
- strandCollapse = FALSE, |
|
| 49 |
- fileType = "cytosineReport", |
|
| 50 |
- verbose = FALSE) |
|
| 51 |
- checkTrue(is(bsseq, "BSseq")) |
|
| 52 |
- # Check that strandCollapse = FALSE works |
|
| 53 |
- checkEquals(length(bsseq), 100L) |
|
| 54 |
- checkTrue("+" %in% strand(bsseq))
|
|
| 55 |
- |
|
| 56 |
- # Check that strandCollapse = TRUE works |
|
| 57 |
- bsseq <- read.bismark(files = infile, |
|
| 58 |
- sampleNames = "test_data", |
|
| 59 |
- rmZeroCov = FALSE, |
|
| 60 |
- strandCollapse = TRUE, |
|
| 61 |
- fileType = "cytosineReport", |
|
| 62 |
- verbose = FALSE) |
|
| 63 |
- checkEquals(length(bsseq), 50L) |
|
| 64 |
- checkTrue(all(strand(bsseq) == "*")) |
|
| 65 |
-} |
|
| 66 |
- |
| ... | ... |
@@ -1,3 +1,49 @@ |
| 1 | 1 |
context("read.bismark")
|
| 2 | 2 |
|
| 3 | 3 |
# TODO: Re-factor read.bismark() and update tests accordingly |
| 4 |
+test_that("read.bismark() works for 'coverage' file", {
|
|
| 5 |
+ infile <- system.file("extdata", "test_data.fastq_bismark.bismark.cov.gz",
|
|
| 6 |
+ package = "bsseq") |
|
| 7 |
+ bsseq <- read.bismark(files = infile, |
|
| 8 |
+ sampleNames = "test_data", |
|
| 9 |
+ rmZeroCov = FALSE, |
|
| 10 |
+ strandCollapse = FALSE, |
|
| 11 |
+ verbose = FALSE) |
|
| 12 |
+ expect_is(bsseq, "BSseq") |
|
| 13 |
+}) |
|
| 14 |
+ |
|
| 15 |
+test_that("read.bismark() works if sampleNames has names", {
|
|
| 16 |
+ # Regression test |
|
| 17 |
+ # Should not fail if sampleNames have names() |
|
| 18 |
+ # TODO: Check why this test is necessary by stepping through read.bismark() |
|
| 19 |
+ bsseq <- read.bismark(files = infile, |
|
| 20 |
+ sampleNames = c(test = "test_data"), |
|
| 21 |
+ rmZeroCov = FALSE, |
|
| 22 |
+ strandCollapse = FALSE, |
|
| 23 |
+ verbose = FALSE) |
|
| 24 |
+ expect_is(bsseq, "BSseq") |
|
| 25 |
+}) |
|
| 26 |
+ |
|
| 27 |
+test_that("read.bismark() works for 'genome wide cytosine report' file", {
|
|
| 28 |
+ # Test that read.bismark() works on good input |
|
| 29 |
+ infile <- system.file("extdata", "test_data.cytosineReport.gz",
|
|
| 30 |
+ package = "bsseq") |
|
| 31 |
+ bsseq <- read.bismark(files = infile, |
|
| 32 |
+ sampleNames = "test_data", |
|
| 33 |
+ rmZeroCov = FALSE, |
|
| 34 |
+ strandCollapse = FALSE, |
|
| 35 |
+ verbose = FALSE) |
|
| 36 |
+ expect_is(bsseq, "BSseq") |
|
| 37 |
+ # Check that strandCollapse = FALSE works |
|
| 38 |
+ expect_equal(nrow(bsseq), 100L) |
|
| 39 |
+ expect_true(all(strand(bsseq) %in% c("+", "-")))
|
|
| 40 |
+ |
|
| 41 |
+ # Check that strandCollapse = TRUE works |
|
| 42 |
+ bsseq <- read.bismark(files = infile, |
|
| 43 |
+ sampleNames = "test_data", |
|
| 44 |
+ rmZeroCov = FALSE, |
|
| 45 |
+ strandCollapse = TRUE, |
|
| 46 |
+ verbose = FALSE) |
|
| 47 |
+ expect_equal(nrow(bsseq), 50L) |
|
| 48 |
+ expect_true(all(strand(bsseq) == "*")) |
|
| 49 |
+}) |
