Nothing
#checks calculation of candidate regions of selection
context("calc_candidate_regions")
setup({
library(rehh.data)
data(wgscan.cgu)
data(wgscan.eut)
})
test_that("checked_calc_candidate_regions", {
sink("test_calc_candidate_regions.log")
ihs.cgu <- ihh2ihs(wgscan.cgu)
cr.ihs.cgu <-
calc_candidate_regions(
ihs.cgu,
threshold = 4,
pval = TRUE,
overlap = 100000,
min_n_extr_mrk = 2,
min_perc_extr_mrk = 20
)
chr_numbers <- as.integer(as.character(cr.ihs.cgu$CHR))
expect_identical(chr_numbers, c(5L, 12L, 18L))
cr.ihs.cgu <-
calc_candidate_regions(
ihs.cgu,
threshold = 4,
pval = TRUE,
overlap = 100000,
min_n_extr_mrk = 2
)
chr_numbers <- as.integer(as.character(cr.ihs.cgu$CHR))
expect_identical(chr_numbers, c(1L, 4L, 5L, 5L, 7L, 12L, 18L))
rsb.cgu_eut <- ines2rsb(wgscan.cgu, wgscan.eut)
cr.rsb.cgu_eut <-
calc_candidate_regions(
rsb.cgu_eut,
threshold = 4,
pval = TRUE,
overlap = 100000,
min_n_extr_mrk = 2
)
chr_numbers <-
as.integer(as.character(cr.rsb.cgu_eut$CHR))
expect_identical(chr_numbers,
c(2L,
3L,
5L,
5L,
5L,
7L,
7L,
10L,
11L,
12L,
13L,
14L,
14L,
16L,
16L,
18L))
xpehh.cgu_eut <- ies2xpehh(wgscan.cgu, wgscan.eut)
cr.xpehh.cgu_eut <-
calc_candidate_regions(
xpehh.cgu_eut,
threshold = 4,
pval = TRUE,
overlap = 100000,
min_n_extr_mrk = 2
)
chr_numbers <-
as.integer(as.character(cr.xpehh.cgu_eut$CHR))
expect_identical(chr_numbers, c(2L, 3L, 5L, 5L, 10L, 12L, 13L, 13L, 14L, 14L, 16L))
## calc_region_stats should yield the same results if applied to the same score
region_stats.cgu <- calc_region_stats(ihs.cgu,
cr.ihs.cgu,
threshold = 4,
pval = TRUE)
expect_identical(cr.ihs.cgu, region_stats.cgu)
sink()
file.remove("test_calc_candidate_regions.log")
})
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