tests/testthat/test_GRBs.R

In CNEr: CNE Detection and Visualization

test_that("test_makeGRBs", {
  # library(TxDb.Drerio.UCSC.danRer10.refGene)
  # refGenesDanRer10 <- genes(TxDb.Drerio.UCSC.danRer10.refGene)
  # ancoraCNEsFns <- file.path(system.file("extdata", package="CNEr"), 
  #                            c("cne2wBf_cypCar1_danRer10_100_100",
  #                              "cne2wBf_cteIde1_danRer10_100_100",
  #                              "cne2wBf_AstMex102_danRer10_48_50"))
  # cneList <- do.call(GRangesList, 
  #                    lapply(ancoraCNEsFns, readAncora, assembly="danRer10"))
  # names(cneList) <- c("Common carp", "Grass carp", "Blind cave fish")
  # seqlengths(cneList) <- seqlengths(TxDb.Drerio.UCSC.danRer10.refGene)[
  #   names(seqlengths(cneList))]
  # danRer10GRBs <- makeGRBs(cneList, winSize=200, genes=refGenesDanRer10,
  #                          ratio=1.2, background="genome")
  # expect_identical(length(danRer10GRBs), 368L)
  # danRer10GRBs <- makeGRBs(cneList, winSize=200, genes=refGenesDanRer10,
  #                          ratio=1.2, background="chromosome")
  # expect_identical(length(danRer10GRBs), 411L)
}
)