tests/testthat/test_annotation.R

In LTLA/fugi: Further Utilities for Genomic Interactions

gi <- GenomicInteractions(
          metadata = list(experiment_name="test", description = "this is a test"),
          anchor1 = as.integer(c(1, 7, 8, 4, 5)),
          anchor2 = as.integer(c(6, 2, 10, 9, 3)),
          regions = GRanges(seqnames = S4Vectors::Rle(factor(c("chr1", "chr2")), c(6, 4)),
                            ranges = IRanges(start = c(1,6,3,4,5,7,2,3,4,5),
                                             width = c(10,9,6,7,6,10,9,8,7,8)),
                            strand = S4Vectors::Rle(c("+", "-", "+", "-"), c(2,4,1,3)),
                            seqinfo = Seqinfo(seqnames = paste("chr", 1:2, sep=""))),
          counts = 1:5)

promoters <- GRanges(seqnames = S4Vectors::Rle(factor(c("chr1", "chr2")), c(2, 1)),
                     ranges = IRanges(c(9, 14, 11), width = 4:6),
                     strand = S4Vectors::Rle(strand(c("+", "-", "-"))),
                     seqinfo = Seqinfo(seqnames = paste("chr", 1:2, sep="")),
                     id = paste0("P", 1:3))

## Annotation by overlaps
annotateInteractions(gi, list(promoter = promoters))

test_that("Annotate interactions returns expected results", {
  expect_node_class_one <- c("promoter", rep("distal", 4))
  expect_node_class_two <- c(rep("promoter", 3), rep("distal", 2))
  
  expect_ids_one <- c("P1", as.list(rep(NA, 4)))
  expect_ids_two <- c(c("P2", "P1","P3", as.list(rep(NA, 2))))
  
  expect_equal(anchorOne(gi)$node.class, expect_node_class_one)
  expect_equal(anchorTwo(gi)$node.class, expect_node_class_two)
  
  expect_equal(anchorOne(gi)$promoter.id, expect_ids_one)
  expect_equal(anchorTwo(gi)$promoter.id, expect_ids_two)
  })

## Annotation by setting mcols

# ## test summarisation
# 
# test_that("summariseByFeatures results are the same as before", {
#   expect_equal_to_reference(summariseByFeatures(gi, promoters, feature.name = "promoter"),
#                             file = "summariseByFeatures.rds")
# })
# 
# test_that("summariseByFeaturePairs results are the same as before", {
#   expect_equal_to_reference( summariseByFeaturePairs(gi, features.one = promoters, features.two = promoters, 
#                                                      feature.name.one = "promoter", feature.name.two = "promoter"),
#                             file = "summariseByFeaturePairs.rds")
# })


## Resetting annotation
resetAnnotations(gi)

test_that("resetting annotations removes mcols", {
  expect_false("signal" %in% names(mcols(anchorOne(gi))))
  expect_false("signal" %in% names(mcols(anchorTwo(gi))))
  
  expect_false("node.class" %in% names(mcols(anchorOne(gi))))
  expect_false("node.class" %in% names(mcols(anchorTwo(gi))))
  
  expect_true(length(mcols(anchorOne(gi)))==0)
  expect_true(length(mcols(anchorTwo(gi)))==0)
})

## Distance calculations

test_that("distance calculations work as expected", {
  expect_equal(calculateDistances(gi),
               c(6, NA, 2, NA, 2))
  expect_equal(calculateDistances(gi, method = "midpoint"),
               c(6, NA, 2, NA, 2))
  expect_equal(calculateDistances(gi, method = "inner"),
               c(-4, NA, -6, NA, -4))
  expect_equal(calculateDistances(gi, method = "outer"),
               c(16, NA, 10, NA, 8))
  expect_error(calculateDistances(gi, method = "my_method"))
})