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# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
# (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text.
# OICR makes no representations whatsoever as to the SOFTWARE contained herein. It is experimental in nature and is provided WITHOUT
# WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION
# OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT.
# By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or
# nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE.
# If publications result from research using this SOFTWARE, we ask that the Ontario Institute for Cancer Research be acknowledged and/or
# credit be given to OICR scientists, as scientifically appropriate.
context("in.region")
if (check.binary("bedtools", verbose = TRUE)) {
test_that("check in.region", {
regions <- get.example.regions()
regions$a <- bedr.sort.region(regions$a)
regions$b <- bedr.sort.region(regions$b)
a.b.overlap <- c(F,T,T,T,F,T,T,F)
b.a.overlap <- c(F,T,F,F,F,T,F)
a.b.overlap.pc0 <- c(F,T,T,T,F,T,T,F)
a.b.overlap.pc5 <- c(F,T,T,T,F,F,T,F)
a.b.overlap.pc1 <- c(F,F,T,T,F,F,T,F)
a.b.overlap.sorted <- c(F,T,T,T,F,T,T,F)
a.b.overlap.merged <- c(F,T,T,T,F,T,F)
# bad region
expect_error(in.region(regions$a, "cat", verbose = F));
expect_error(in.region(regions$a, regions$d, verbose = F));
# raw
expect_equal(in.region(regions$a, regions$b, verbose = F), a.b.overlap);
# reverse a/b
expect_equal(in.region(regions$b, regions$a, verbose = F), b.a.overlap);
# vary the proportion over overlap
expect_equal(in.region(regions$a, regions$b, proportion.overlap = 0.1, verbose = F), a.b.overlap.pc0);
expect_equal(in.region(regions$a, regions$b, proportion.overlap = .5, verbose = F), a.b.overlap.pc5);
expect_equal(in.region(regions$a, regions$b, proportion.overlap = 1, verbose = F), a.b.overlap.pc1);
# sorted
expect_equal(in.region(bedr.sort.region(regions$a, verbose = FALSE), regions$b, verbose=F), a.b.overlap.sorted)
# merged
expect_equal(in.region(bedr.merge.region(regions$a,verbose=F, distance = -1), regions$b, verbose=F), a.b.overlap.merged)
# %in.region% gives same results
expect_equal(in.region(regions$a,regions$b, verbose = F), regions$a %in.region% regions$b)
})
}
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