Nothing
context("subset kinship matrices")
test_that("subset.kinship works", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron[c("2","3","4","5","6","7"), 2:6]
pr <- calc_genoprob(iron)
k <- calc_kinship(pr)
k_loco <- calc_kinship(pr, "loco")
# subset by individuals
expect_equal(subset_kinship(k, ind=c(2,4)), k[c(2,4), c(2,4)])
expect_equal(subset_kinship(k, ind=c("2","4")), k[c("2","4"), c("2","4")])
# subset by individuals, loco case
expect_equal(subset_kinship(k_loco, ind=c(2,4)), lapply(k_loco, function(a) a[c(2,4), c(2,4)]))
expect_equal(subset_kinship(k_loco, ind=c("2","4")), lapply(k_loco, function(a) a[c("2","4"), c("2","4")]))
# chr argument ignored if a plain matrix
expect_equal(subset_kinship(k, ind=c(2,4), chr=5), k[c(2,4), c(2,4)])
expect_equal(subset_kinship(k, ind=c("2","4"), chr=5), k[c("2","4"), c("2","4")])
# chr argument, loco case, one chr in result
expect_equal(subset_kinship(k_loco, ind=c(2,4), chr=5), k_loco[["5"]][c(2,4), c(2,4)])
expect_equal(subset_kinship(k_loco, ind=c("2","4"), chr=5), k_loco[["5"]][c("2","4"), c("2","4")])
# chr argument, loco case, mult chr in result
expect_equal(subset_kinship(k_loco, ind=c(2,4), chr=c(2,5)), lapply(k_loco[c("2","5")], function(a) a[c(2,4), c(2,4)]))
expect_equal(subset_kinship(k_loco, ind=c("2","4"), chr=c(2,5)), lapply(k_loco[c("2", "5")], function(a) a[c("2","4"), c("2","4")]))
# chr argument, loco case, negative subscripts
expect_equal(subset_kinship(k_loco, ind=c(2,4), chr=-c(2,4)), lapply(k_loco[c("3","5","6")], function(a) a[c(2,4), c(2,4)]))
expect_equal(subset_kinship(k_loco, ind=c("2","4"), chr=c("-2","-4")), lapply(k_loco[c("3","5","6")], function(a) a[c("2","4"), c("2","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.