Nothing
context("Calculate heterozygosities")
test_that("calc_het works for an intercross", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
pr <- calc_genoprob(iron, err=0.002)
# omit_x works?
expect_equal(calc_het(pr[,1:19]), calc_het(pr, omit_x=TRUE))
expect_equal(calc_het(pr[,1:19], "marker"), calc_het(pr, "marker", omit_x=TRUE))
# by individual
ind <- c(88,105,231)
expected <- c(`88` = 0.437768300719857, `105` = 0.530653642640462, `231` = 0.51155729816745)
expect_equal(calc_het(pr[ind,]), expected)
expect_equal(calc_het(pr[ind,], omit_x=TRUE), expected)
expected_wX <- c(`88` = 0.424502594637437, `105` = 0.514573229227115, `231` = 0.526341691848004)
expect_equal(calc_het(pr[ind,], omit_x=FALSE), expected_wX)
# by marker
expected <- c(D19Mit68 = 0.48461632550778, D19Mit37 = 0.477608930381241,
DXMit16 = 0.251799101291949, DXMit186 = 0.258740713762659)
expect_equal(calc_het(pr[,c(19,"X")], "marker"), expected[1:2])
expect_equal(calc_het(pr[,c(19,"X")], "marker", omit_x=TRUE), expected[1:2])
expect_equal(calc_het(pr[,c(19,"X")], "marker", omit_x=FALSE), expected)
})
test_that("calc_het works with multi-core", {
skip_if(isnt_karl(), "this test only run locally")
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
pr <- calc_genoprob(iron, err=0.002)
# test multicore
expect_equal(calc_het(pr), calc_het(pr, cores=4))
expect_equal(calc_het(pr, "marker"), calc_het(pr, "marker", cores=4))
expect_equal(calc_het(pr, omit_x=FALSE), calc_het(pr, omit_x=FALSE, cores=4))
expect_equal(calc_het(pr, "marker", omit_x=FALSE), calc_het(pr, "marker", omit_x=FALSE, cores=4))
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.