if (suppressMessages(suppressWarnings(require(BEDMatrix)))) {
# loads Rdata matrices to test
load('Xs.RData')
rm(X) # pretend we don't have X!
# load the BED X instead
X <- suppressMessages(suppressWarnings(BEDMatrix('Xs')))
# only repeat tests where genotypes X is input!
test_that("function returns precomputed values: popkin_A", {
expect_silent( obj <- popkin_A( X ) )
expect_equal( obj$A, A )
expect_equal( obj$M, M )
})
# higher-level tests now!
test_that("function returns precomputed values: popkin", {
expect_equal(popkin(X), Phi0)
expect_equal(popkin(X, subpops0), Phi0)
expect_equal(popkin(X, subpops), Phi)
})
test_that("popkin preserves names of individuals", {
# in this case X is the wide matrix (individuals along rows)
expect_equal(rownames(X), colnames(Phi))
expect_equal(rownames(X), rownames(Phi))
})
}
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