Further simplify examples and tests related to lawremi/rtracklayer#83

leekgroup · May 21, 2024 · 7e903b0 · 7e903b0
1 parent aaa0947
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Showing 5 changed files with 59 additions and 56 deletions.
diff --git a/R/coverage_matrix.R b/R/coverage_matrix.R
@@ -55,15 +55,20 @@
 #' @examples
 #'
 #' if (.Platform$OS.type != "windows") {
+#'     ## Workaround for https://github.com/lawremi/rtracklayer/issues/83
+#'     download_study("SRP002001", type = "mean")
+#'     download_study("SRP002001", type = "samples")
+#'
 #'     ## Reading BigWig files is not supported by rtracklayer on Windows
 #'     ## Define expressed regions for study DRP002835, chrY
-#'     regions <- expressed_regions("DRP002835", "chrY",
+#'     regions <- expressed_regions("SRP002001", "chrY",
 #'         cutoff = 5L,
-#'         maxClusterGap = 3000L
+#'         maxClusterGap = 3000L,
+#'         outdir = "SRP002001"
 #'     )
 #'
 #'     ## Now calculate the coverage matrix for this study
-#'     rse <- coverage_matrix("DRP002835", "chrY", regions)
+#'     rse <- coverage_matrix("SRP002001", "chrY", regions, outdir = "SRP002001")
 #'
 #'     ## One row per region
 #'     identical(length(regions), nrow(rse))

diff --git a/R/expressed_regions.R b/R/expressed_regions.R
@@ -37,17 +37,21 @@
 #' [railMatrix][derfinder::railMatrix]
 #'
 #' @examples
-#' ## Define expressed regions for study SRP009615, chrY
+#' ## Define expressed regions for study DRP002835, chrY
 #' if (.Platform$OS.type != "windows") {
+#'     ## Workaround for https://github.com/lawremi/rtracklayer/issues/83
+#'     download_study("SRP002001", type = "mean")
+#'
 #'     ## Reading BigWig files is not supported by rtracklayer on Windows
-#'     regions <- expressed_regions("SRP009615", "chrY",
+#'     regions <- expressed_regions("SRP002001", "chrY",
 #'         cutoff = 5L,
-#'         maxClusterGap = 3000L
+#'         maxClusterGap = 3000L,
+#'         outdir = "SRP002001"
 #'     )
 #' }
 #' \dontrun{
 #' ## Define the regions for multiple chrs
-#' regs <- sapply(chrs, expressed_regions, project = "SRP009615", cutoff = 5L)
+#' regs <- sapply(chrs, expressed_regions, project = "SRP002001", cutoff = 5L)
 #'
 #' ## You can then combine them into a single GRanges object if you want to
 #' library("GenomicRanges")

diff --git a/man/coverage_matrix.Rd b/man/coverage_matrix.Rd
diff --git a/man/expressed_regions.Rd b/man/expressed_regions.Rd
diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
@@ -109,53 +109,38 @@ test_that("Scaling", {
 })
 
 if (.Platform$OS.type != "windows") {
-    range <-
-        GRanges(seqnames = "chrY", ranges = IRanges(1, 57227415))
-    output <-
-        tryCatch(
-            rtracklayer::import(
-                "http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw",
-                selection = reduce(range),
-                as = "RleList"
-            ),
-            error = identity
+    regions <- expressed_regions("SRP002001", "chrY", cutoff = 5, outdir = tmpdir)
+    ## Artificially remove the mean coverage file so that the file will have to
+    ## get downloaded on the first test, then it'll be present for the second
+    ## test
+    unlink(localfiles["mean_SRP002001.bw"])
+
+    test_that("Expressed regions", {
+        expect_equal(
+            regions,
+            expressed_regions("SRP002001", "chrY", cutoff = 5, outdir = tmpdir)
         )
-    if (inherits(output, "error")) {
-        warning("Remote BigWig file access is failing. See https://github.com/lawremi/rtracklayer/issues/83 for more details.")
-    } else {
-        regions <- expressed_regions("SRP002001", "chrY", cutoff = 5)
-        ## Artificially remove the mean coverage file so that the file will have to
-        ## get downloaded on the first test, then it'll be present for the second
-        ## test
-        unlink(localfiles["mean_SRP002001.bw"])
-
-        test_that("Expressed regions", {
-            expect_equal(
-                regions,
-                expressed_regions("SRP002001", "chrY", cutoff = 5, outdir = tmpdir)
-            )
-        })
+    })
 
 
-        rse_ER <- coverage_matrix("SRP002001", "chrY", regions)
-        ## Same for the phenotype data and the sample bigwig file
-        unlink(localfiles["SRP002001.tsv"])
-        unlink(localfiles["SRR036661.bw"])
+    rse_ER <- coverage_matrix("SRP002001", "chrY", regions, outdir = tmpdir)
+    ## Same for the phenotype data and the sample bigwig file
+    unlink(localfiles["SRP002001.tsv"])
+    unlink(localfiles["SRR036661.bw"])
 
-        test_that("Coverage matrix", {
-            expect_equal(
-                rse_ER,
-                coverage_matrix("SRP002001", "chrY", regions, outdir = tmpdir)
-            )
-            expect_equal(
-                rse_ER,
-                coverage_matrix("SRP002001", "chrY", regions,
-                    outdir = tmpdir,
-                    chunksize = 500
-                )
+    test_that("Coverage matrix", {
+        expect_equal(
+            rse_ER,
+            coverage_matrix("SRP002001", "chrY", regions, outdir = tmpdir)
+        )
+        expect_equal(
+            rse_ER,
+            coverage_matrix("SRP002001", "chrY", regions,
+                outdir = tmpdir,
+                chunksize = 500
             )
-        })
-    }
+        )
+    })
 }
 
 ## Check size once: