library("testthat")
context("Test kernel calculation")
test_that("Test network kernel calculation and dimension", {
# saved data
data(net.kernel.hsa04020)
# derivation
data(gwas)
data(hsa04020)
net_kernel <- calc_kernel(gwas, hsa04020, knots=NULL, type='net', calculation='cpu')
expect_equal(dim(net_kernel@kernel)[1],dim(gwas@geno)[1])
expect_equal(dim(net_kernel@kernel)[2],dim(gwas@geno)[1])
expect_equal(dim(net_kernel@kernel), dim(net.kernel.hsa04020@kernel))
expect_equal(net_kernel@kernel, net.kernel.hsa04020@kernel)
})
test_that("Test lowrank kernel dimension", {
data(gwas)
data(hsa04020)
square <- calc_kernel(gwas, hsa04020, knots=gwas, type='lin', calculation='cpu')
dim(square@kernel)
gwas2 <- new('GWASdata', pheno=pheno[1:10,], geno=geno[1:10,], anno=anno, desc="study 2")
low_rank <- calc_kernel(gwas, hsa04020, knots = gwas2, type='net', calculation='cpu')
dim(low_rank@kernel)
expect_equal(dim(low_rank@kernel)[1],dim(gwas@geno)[1])
expect_equal(dim(low_rank@kernel)[2],dim(gwas2@geno)[1])
})
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