fix: tests for pair_granges

js2264 · Jun 19, 2024 · 59b02c0 · 59b02c0
1 parent eec32cb
commit 59b02c0
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Showing 4 changed files with 13 additions and 11 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -240,6 +240,7 @@ importFrom(plyranges,anchor_5p)
 importFrom(plyranges,anchor_center)
 importFrom(plyranges,anchor_end)
 importFrom(plyranges,anchor_start)
+importFrom(plyranges,as_granges)
 importFrom(plyranges,count_overlaps)
 importFrom(plyranges,count_overlaps_directed)
 importFrom(plyranges,filter_by_non_overlaps)

diff --git a/R/pair-granges.R b/R/pair-granges.R
@@ -27,6 +27,6 @@
 pair_granges <- function(x) {
 
     combs <- combn(length(x), 2)
-    InteractionSet::GInteractions(combs[1,], combs[2,], gr)
+    InteractionSet::GInteractions(combs[1,], combs[2,], x)
 
 }
diff --git a/R/reexports-plyranges.R b/R/reexports-plyranges.R
@@ -1,4 +1,5 @@
 #' @rdname reexports
+#' @importFrom plyranges as_granges
 #' @importFrom plyranges anchor
 #' @export
 plyranges::anchor

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -10,15 +10,15 @@ library(testthat)
 library(plyinteractions)
 
 gi <- read.table(text = "
-        chr1 11 20 chr1 21 30 + +
-        chr1 11 20 chr1 51 55 + +
-        chr1 11 30 chr1 51 55 - -
-        chr1 11 30 chr2 51 60 - -",
-        col.names = c(
-        "seqnames1", "start1", "end1", 
-        "seqnames2", "start2", "end2", "strand1", "strand2")
-    ) |> 
-        as_ginteractions() |> 
-        mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans'))
+    chr1 11 20 chr1 21 30 + +
+    chr1 11 20 chr1 51 55 + +
+    chr1 11 30 chr1 51 55 - -
+    chr1 11 30 chr2 51 60 - -",
+    col.names = c(
+    "seqnames1", "start1", "end1", 
+    "seqnames2", "start2", "end2", "strand1", "strand2")
+) |> 
+    as_ginteractions() |> 
+    mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans'))
 
 test_check("plyinteractions")