data(BS.cancer.ex, package = 'bsseqData')
small_test = BS.cancer.ex[1:10]
expected_cov_cancer2_normal2 = bsseq::getCoverage(small_test, type = 'Cov')[c(3,4,7,8,9,10), ]
expected_meth_cancer2_normal2 = bsseq::getCoverage(small_test, type = 'M')[c(3,4,7,8,9,10), ]
expected_cov_cancer2_normal3 = bsseq::getCoverage(small_test, type = 'Cov')[c(3,8,9), ]
expected_meth_cancer2_normal3 = bsseq::getCoverage(small_test, type = 'M')[c(3,8,9), ]
expected_cov_cancer3_normal3 = bsseq::getCoverage(small_test, type = 'Cov')[c(3,8), ]
expected_meth_cancer3_normal3 = bsseq::getCoverage(small_test, type = 'M')[c(3,8), ]
#####################################
test_that('bs missing check', {
expect_error(
filter_loci_by_group_coverage(),
'Must pass bs as a BSseq object',
fixed = TRUE
)
})
test_that('group_column missing check', {
expect_error(
filter_loci_by_group_coverage(bs = small_test),
'Must pass group_column as a character string',
fixed = TRUE
)
})
test_that('min_samples_per_group missing check', {
expect_error(
filter_loci_by_group_coverage(bs = small_test, group_column = 'Type'),
'Must pass min_samples_per_group as a named integer vector',
fixed = TRUE
)
})
#####################################
test_that('bs type check', {
expect_error(
filter_loci_by_group_coverage(
bs = 'a',
group_column = 'Type',
c('cancer' = 3, 'normal' = 3)),
'bs must be class BSseq',
fixed = TRUE
)
})
test_that('group_column type check', {
expect_error(
filter_loci_by_group_coverage(
bs = small_test,
group_column = 6,
c('cancer' = 3, 'normal' = 3)),
'group_column must be a character string',
fixed = TRUE
)
})
test_that('min_samples_per_group type check', {
expect_error(
filter_loci_by_group_coverage(
bs = small_test,
group_column = 'Type',
c('cancer' = 'a', 'normal' = 3)),
'min_samples_per_group must be a named integer vector',
fixed = TRUE
)
})
#####################################
test_that('Valid group_column name check', {
expect_error(
filter_loci_by_group_coverage(
bs = small_test,
group_column = 'blue',
c('cancer' = 3, 'normal' = 3)),
'group_column: blue not in column names of pData', # () seem to be a problem
fixed = TRUE
)
})
test_that('Valid factor name check', {
expect_error(
filter_loci_by_group_coverage(
bs = small_test,
group_column = 'Type',
c('blue' = 3, 'normal' = 3)),
'Not all names of min_samples_per_group are in group_column',
fixed = TRUE
)
})
test_that('All loci removed check', {
expect_error(
filter_loci_by_group_coverage(
bs = small_test,
group_column = 'Type',
c('cancer' = 4, 'normal' = 4)),
'Thresholds for the following groups were too strict'
)
})
#####################################
test_that('Test cancer 2 normal 2', {
test = filter_loci_by_group_coverage(
bs = small_test,
group_column = 'Type',
c('cancer' = 2, 'normal' = 2))
expect_equivalent(
bsseq::getCoverage(test, type = 'Cov'),
expected_cov_cancer2_normal2
)
expect_equivalent(
bsseq::getCoverage(test, type = 'M'),
expected_meth_cancer2_normal2
)
})
test_that('Test cancer 2 normal 3', {
test = filter_loci_by_group_coverage(
bs = small_test,
group_column = 'Type',
c('cancer' = 2, 'normal' = 3))
expect_equivalent(
bsseq::getCoverage(test, type = 'Cov'),
expected_cov_cancer2_normal3
)
expect_equivalent(
bsseq::getCoverage(test, type = 'M'),
expected_meth_cancer2_normal3
)
})
test_that('Test cancer 3 normal 3', {
test = filter_loci_by_group_coverage(
bs = small_test,
group_column = 'Type',
c('cancer' = 3, 'normal' = 3))
expect_equivalent(
bsseq::getCoverage(test, type = 'Cov'),
expected_cov_cancer3_normal3
)
expect_equivalent(
bsseq::getCoverage(test, type = 'M'),
expected_meth_cancer3_normal3
)
})
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