roll back expand methods and test to use S4vectors List methods

R/ranges-expand.R

@@ -23,15 +23,15 @@
 #' @examples
 #' grng <- as_granges(data.frame(seqnames = "chr1", start = 20:23, width = 1000))
 #' grng <- mutate(grng, 
-#'                exon_id = List(a = 1, b = c(4,5), c = 3, d = c(2,5))
+#'                exon_id = IntegerList(a = 1, b = c(4,5), c = 3, d = c(2,5))
 #'                )
 #' grng                
 #' expand_ranges(grng)
 #' expand_ranges(grng, .id = "name")
 #' 
 #' # empty list elements are not preserved by default
 #' grng <- mutate(grng, 
-#'                exon_id = List(a = NULL, b = c(4,5), c= 3, d = c(2,5))
+#'                exon_id = IntegerList(a = NULL, b = c(4,5), c= 3, d = c(2,5))
 #'                )
 #' expand_ranges(grng)
 #' expand_ranges(grng, .keep_empty = TRUE)
@@ -101,7 +101,7 @@ expand_ranges <- function(data, ..., .drop = FALSE, .id = NULL, .keep_empty = FA
 
 
 get_list_cols <- function(data) {
-  list_cols_pos <- unlist(Map(function(.) is(., "list"), mcols(data)))
+  list_cols_pos <- unlist(Map(function(.) is(., "List"), mcols(data)))
 
   list_cols <- Filter(isTRUE, list_cols_pos)
 

tests/testthat/test-unnest.R

@@ -12,9 +12,10 @@ test_that("expanding makes sense", {
 
   # by default expand_ranges does cartesian product of list columns
   gr <- as_granges(data.frame(seqnames = "chr1", start = 20:22, width = 1000))
+
   gr <- mutate(gr,
-                 col1 = List(a = 1L, b = c(4L,5L), c = c(2L,3L)),
-                 col2 = List(c(1L,2L), c(3L,4L), c(5L)),
+                 col1 = IntegerList(a = 1L, b = c(4L,5L), c = c(2L,3L)),
+                 col2 = IntegerList(c(1L,2L), c(3L,4L), c(5L)),
                  score = 1:3)
 
   correct_gr <- GRanges(seqnames = "chr1",
@@ -23,6 +24,7 @@ test_that("expanding makes sense", {
                         col1 = c(1L,1L,4L,4L,5L,5L,2L,3L),
                         col2 = c(1L,2L,3L,4L,3L,4L,5L,5L),
                         score = c(1L,1L,2L,2L,2L,2L,3L,3L))
+
   test_gr <- expand_ranges(gr, .recursive = TRUE)
 
   expect_identical(correct_gr, test_gr)
@@ -43,7 +45,7 @@ test_that("expanding makes sense", {
                           ranges = IRanges(start = c(20,21,21,22,22),
                                            width = 1000),
                           col1 = as.integer(c(1,4,5,2,3)),
-                          col2 = I(list(c(1L,2L), c(3L,4L), c(3L,4L), 5L,5L)),
+                          col2 = IntegerList(c(1L,2L), c(3L,4L), c(3L,4L), 5L,5L),
                           score = as.integer(c(1,2,2,3,3)))
   test_gr <- expand_ranges(gr, col1)
   expect_identical(correct_gr, test_gr)
@@ -76,15 +78,15 @@ test_that("expanding makes sense", {
                         ranges = IRanges(start = c(20,21,21,22,22),
                                          width = 1000),
                         col1 = as.integer(c(1,4,5,2,3)),
-                        col2 = I(list(c(1L,2L), c(3L,4L), c(3L,4L), 5L,5L)),
+                        col2 = IntegerList(c(1L,2L), c(3L,4L), c(3L,4L), 5L,5L),
                         score = as.integer(c(1,2,2,3,3)),
                         id1 = c("a", "b", "b", "c", "c"))
   test_gr <- expand_ranges(gr, col1, .id = "id1", .recursive = TRUE)
   expect_identical(correct_gr, test_gr)
 
   # one column test
   gr <- as_granges(data.frame(seqnames = "chr1", start = 20:22, width = 1000))
-  gr <- mutate(gr, col1 = list(a = 1, b = c(4,5), c = c(2,3)))
+  gr <- mutate(gr, col1 = IntegerList(a = 1, b = c(4,5), c = c(2,3)))
   correct_gr <- S4Vectors::expand(gr)
   expect_equal(expand_ranges(gr), correct_gr)
 
@@ -93,7 +95,7 @@ test_that("expanding makes sense", {
 
   # drop emptys
   gr <- as_granges(data.frame(seqnames = "chr1", start = 20:22, width = 1000))
-  gr <- mutate(gr, col1 = list(a = integer(), b = c(4,5), c = c(2,3)))
+  gr <- mutate(gr, col1 = IntegerList(a = integer(), b = c(4,5), c = c(2,3)))
   correct_gr <- S4Vectors::expand(gr, keepEmptyRows = TRUE)
   expect_equal(expand_ranges(gr, .keep_empty = TRUE), correct_gr)
   correct_gr$id1 <- c("a", "b", "b", "c", "c")