tests/testthat/test-normalization.R

In dongzhuoer/rexseek: Matrix Processing in the exSeek Project

testthat::context('Testing normalization')
setwd(here::here(''))  # workspace is reset per file


# normalize ------------------------------------

testthat::test_that('normalize() check args', {
	testthat::expect_error(
		normalize(tempfile(), 'CPM_top'),
		'top_n must be specified for CPM_top method'
	)
	testthat::expect_error(
		normalize(tempfile(), 'CPM_rm'),
		'rm_gene_type must be specified for CPM_rm method'
	)
	testthat::expect_error(
		normalize(tempfile(), 'CPM_refer'),
		'refer_gene_id must be specified for CPM_refer method'
	)
})



# norm_SCnorm ----------------------
testthat::test_that('norm_SCnorm()', {
	mat_SCnorm <- suppressMessages(norm_SCnorm(sim_mat*10))

	testthat::expect_true(is.matrix(mat_SCnorm))
	testthat::expect_identical(dim(mat_SCnorm), dim(sim_mat))
})

# norm_tmm ----------------------
testthat::test_that('norm_tmm()', {
	testthat::expect_identical(suppressWarnings(norm_tmm(sim_mat)), sim_mat)
    testthat::expect_warning(
        suppressMessages(norm_tmm(sim_mat)), 
        "norm_tmm() is deprecated, returning the original matrix.", 
        fixed = TRUE
    )
    testthat::expect_message(
        suppressWarnings(norm_tmm(sim_mat)), 
        'scater::normaliseExprs(., "TMM")', 
        fixed = TRUE
    )
})

# norm_rle ----------------------
testthat::test_that('norm_rle()', {
	testthat::expect_identical(suppressWarnings(norm_rle(sim_mat)), sim_mat)
    testthat::expect_warning(
        suppressMessages(norm_rle(sim_mat)), 
        "norm_rle() is deprecated, returning the original matrix.", 
        fixed = TRUE
    )
    testthat::expect_message(
        suppressWarnings(norm_rle(sim_mat)), 
        'scater::normaliseExprs(., "RLE")', 
        fixed = TRUE
    )
})

# norm_cpm_total ----------------------
testthat::test_that('norm_cpm_total()', {
	mat_cpm <- norm_cpm_total(sim_mat)

	testthat::expect_true(is.matrix(mat_cpm))
	testthat::expect_identical(dim(mat_cpm), dim(sim_mat))
})

# norm_cpm_top ----------------------
testthat::test_that('norm_cpm_top()', {
	mat_cpm_top <- norm_cpm_top(sim_mat, 20)

	testthat::expect_true(is.matrix(mat_cpm_top))
	testthat::expect_identical(dim(mat_cpm_top), dim(sim_mat))
})

testthat::test_that('norm_cpm_top() error', {
	norm_cpm_top(sim_mat, nrow(sim_mat))

	testthat::expect_error(
		norm_cpm_top(sim_mat, nrow(sim_mat) + 1),
		'too few feature for CPM top n normalization'
	)
})

# norm_cpm_rm -----------------
testthat::test_that('norm_cpm_rm()', {
	mat_cpm_rm <- norm_cpm_rm(sim_mat, c('miRNA', 'piRNA'))

	testthat::expect_true(is.matrix(mat_cpm_rm))
	testthat::expect_identical(dim(mat_cpm_rm), dim(sim_mat))
})


testthat::test_that('norm_cpm_rm()', {
	norm_cpm_rm(sim_mat, 'lncRNA')

	testthat::expect_error(
		norm_cpm_rm(sim_mat, 'noRNA'),
		'unknown transcript type to remove for CPM normalization'
	)
})

# norm_cpm_refer -----------------
testthat::test_that('norm_cpm_refer()', {
	mat_cpm_refer <- norm_cpm_refer(sim_mat, suggest_refer$id)

	testthat::expect_true(is.matrix(mat_cpm_refer))
	testthat::expect_identical(dim(mat_cpm_refer), dim(sim_mat))
})


testthat::test_that('norm_cpm_refer()', {
	# test only one reference gene
	norm_cpm_refer(sim_mat, rownames(sim_mat)[1])

	testthat::expect_error(
		norm_cpm_refer(sim_mat, 'non-exist-RNA'),
		'can\'t find any reference genes in the matrix for CPM normalization'
	)
})