test_that('HRSIP runs with default',{
## basic call
df_l2fc = HRSIP(physeq_S2D2_l[[1]],
sparsity_threshold = c(0,0.15,0.3), # limited thresholds to speed up tests
design=~Substrate)
expect_is(df_l2fc, 'data.frame')
expect_gt(nrow(df_l2fc), 0)
df_l2fc_s = df_l2fc %>%
dplyr::group_by(sparsity_threshold,
density_min, density_max) %>%
dplyr::summarize(n = n())
expect_gt(nrow(df_l2fc_s), 1)
})
test_that('HRSIP runs padj_cutoff',{
skip_on_cran()
## basic call
df_l2fc = HRSIP(physeq_S2D2_l[[1]],
design=~Substrate,
sparsity_threshold = c(0,0.15,0.3), # limited thresholds to speed up tests
padj_cutoff=0.1)
expect_is(df_l2fc, 'data.frame')
expect_gt(nrow(df_l2fc), 0)
df_l2fc_s = df_l2fc %>%
dplyr::group_by(sparsity_threshold,
density_min, density_max) %>%
dplyr::summarize(n = n())
expect_equal(nrow(df_l2fc_s), 1)
})
test_that('MW-HR-SIP runs with default & parallel ',{
skip_on_cran()
doParallel::registerDoParallel(2)
windows = data.frame(density_min=c(1.70, 1.72), density_max=c(1.73, 1.75))
df_l2fc = HRSIP(physeq_S2D2_l[[1]],
design=~Substrate,
sparsity_threshold = c(0,0.15,0.3), # limited thresholds to speed up tests
density_windows=windows,
parallel=TRUE)
expect_is(df_l2fc, 'data.frame')
expect_gt(nrow(df_l2fc), 0)
df_l2fc_s = df_l2fc %>%
dplyr::group_by(sparsity_threshold,
density_min, density_max) %>%
dplyr::summarize(n = n())
expect_gt(nrow(df_l2fc_s), 1)
})
test_that('MW-HR-SIP runs with padj_cutoff',{
skip_on_cran()
doParallel::registerDoParallel(2)
windows = data.frame(density_min=c(1.70, 1.72), density_max=c(1.73, 1.75))
df_l2fc = HRSIP(physeq_S2D2_l[[1]],
design=~Substrate,
density_windows=windows,
padj_cutoff=0.1,
parallel=TRUE)
expect_is(df_l2fc, 'data.frame')
expect_gt(nrow(df_l2fc), 0)
df_l2fc_s = df_l2fc %>%
dplyr::group_by(sparsity_threshold, density_min, density_max) %>%
dplyr::summarize(n = n())
expect_equal(nrow(df_l2fc_s), 2)
})
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