tests/testthat/test_colToRanges.R

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

sq <- Seqinfo("chr1", 100, FALSE, "test")
x <- GRanges(c("chr1:1-10", "chr1:6-15", "chr1:51-60"), seqinfo = sq)
df <- data.frame(logFC = rnorm(3), logCPM = rnorm(3,8), p = 10^-rexp(3))
gr <- mergeByCol(x, df, col = "logCPM", pval = "p")
metadata(gr) <- list(check = TRUE)

test_that("Coercion is correct where it should be", {
  new_gr <- colToRanges(gr, "keyval_range")
  expect_s4_class(new_gr, "GRanges")
  expect_true(metadata(new_gr)$check)
  expect_equal(
    colnames(mcols(new_gr)),
    c("n_windows", "n_up", "n_down", "logCPM", "logFC", "p", "p_fdr")
  )
  expect_equal(length(new_gr), 2)
  df$gr <- as.character(x)
  ## Now try using a df
  new_gr <- colToRanges(df, "gr", seqinfo = sq)
  expect_s4_class(new_gr, "GRanges")
  expect_equal(seqinfo(new_gr), sq)
})

test_that("Coercion fails where it should", {
  expect_error(colToRanges(x, ""))
  expect_error(colToRanges(df, "logFC"))
})

test_that("S3 list columns are coerced", {
    tbl <- tibble(range = "chr1:1", list = list(1))
    gr <- colToRanges(tbl, "range")
    expect_true(is(gr$list, "NumericList"))
    # Coercion chould conserve all information & be reversible
    expect_equal(
        tbl,
        as_tibble(colToRanges(tbl, "range"))
    )
})

test_that("Mismatched seqinfo order is handled", {
    sq <- Seqinfo(seqnames = c("chr1", "chr2", "chr3"))
    df <- DataFrame(
        a = c("a", "b"),
        range = c("chr2:1", "chr1:10"),
        gr = GRanges(c("chr2:1", "chr1:10"))
    )
    gr <- colToRanges(df, "range", sq)
    expect_true(is(gr, "GRanges"))
    expect_equal(length(gr), 2)
    expect_equal(length(seqlevels(gr)), 3)
    # colToRanges(df, "gr", sq)
})