tests/testthat/test_recurrentDeletions.R

In cancer-genomics/trellis: Somatic structural variant analysis

context("recurrent deletions")

test_that("recurrentDeletions", {
  genes <- GRanges("chr1", IRanges(5, 10))
  genes$gene_name <- "a"
  gr1 <- GRanges(rep("chr1", 2), IRanges(c(4, 8), c(6, 10)), id=rep("id1", 2))
  gr2 <- GRanges("chr1", IRanges(3, 9), id="id2")
  grl <- GRangesList(id1=gr1, id2=gr2)
  ans <- recurrentDeletions(genes, grl, maxgap=5)
  tab <- summarizeGeneFreq(ans)
  ## should only count first sample once
  expect_identical(tab$frequency, 2L)

  ## gaps allowed
  genes <- GRanges("chr1", IRanges(50e3, 55e3))
  genes$gene_name <- "a"
  gr1 <- GRanges(rep("chr1", 2), IRanges(c(48e3, 60.1e3), c(49e3, 65e3)), id=rep("id1", 2))
  gr2 <- GRanges("chr1", IRanges(50e3, 50e3), id="id2")
  grl <- GRangesList(id1=gr1, id2=gr2)
  ans <- recurrentDeletions(genes, grl, maxgap=5000)
  tab <- summarizeGeneFreq(ans)
  expect_identical(tab$frequency, 2L)

  ## genes that are not recurrent (count of 1) are not returned
  ans <- recurrentDeletions(genes, grl, maxgap=0)
  tab <- summarizeGeneFreq(ans)
  expect_identical(tab$freq, integer())

  ## multiple transcripts for single gene
  genes <- GRanges(c("chr1", "chr1"),  IRanges(c(50e3, 51e3), c(55e3, 56e3)), gene_name=rep("a", 2))
  gr1 <- GRanges(rep("chr1", 2), IRanges(c(48e3, 60.1e3), c(49e3, 65e3)), id=rep("id1", 2))
  gr2 <- GRanges("chr1", IRanges(50e3, 50e3), id="id2")
  grl <- GRangesList(id1=gr1, id2=gr2)
  ans <- recurrentDeletions(genes, grl, maxgap=2000)
  tab <- summarizeGeneFreq(ans)
  expect_identical(tab$freq, 2L)
})

.test_that <- function(nm, expr) NULL

.test_that("annotateRecurrent", {

})