tests/testthat/test-IntronRetention.R

In pachterlab/kma: KeepMeAround: Intron Retention Detection in RNA-Seq data

# context('Intron Retention')
#
# test_that('construction',
#     {
#
#         i2t <- data.frame(
#             intron = c('i1', 'i2', 'i3', 'i3', 'i1'),
#             target_id = c('t1', 't1', 't4', 't1', 't2'),
#             gene = c('g1', 'g2', 'g1', 'g1', 'g1'),
#             intron_extension = c('i1_ext', 'i2_ext', 'i3_ext', 'i3_ext',
#                 'i1_ext'),
#             stringsAsFactors = F)
#
#         targExp <- data.frame(
#             samp1 = c(1, 0.5, 4, 1, 0, 10, 2),
#             samp2 = c(1, 0.25, 0, 2, 8, 3, 3),
#             target_id = c('i1_ext', 'i2_ext', 't1', 't2', 't3', 't4', 'i3_ext'),
#             stringsAsFactors = F)
#
#         ir <- newIntronRetention(targExp, i2t, factor(c('c1', 'c2')), FALSE)
#
#         expect_equal(rownames(ir@numerator), rownames(ir@denominator))
#
#         expect_equal(ir@numerator$samp1, c(1, 0.5, 2), tolerance = 0.01)
#         expect_equal(ir@numerator$samp2, c(1, 0.25, 3), tolerance = 0.01)
#         expect_equal(ir@retention$samp1, c(1 / (4 + 1), 0.5 / 4, 2 / (10 + 4)),
#             tolerance = 0.01)
#         expect_equal(ir@retention$samp2, c(1 / (0 + 2), 0.25 / 0, 3 / (3 + 0)),
#             tolerance = 0.01)
#
#         ir <- newIntronRetention(targExp, i2t, factor(c('c1', 'c2')), TRUE)
#         expect_equal(ir@numerator$samp1, c(1, 0.5, 2), tolerance = 0.01)
#         expect_equal(ir@numerator$samp2, c(1, 0.25, 3), tolerance = 0.01)
#         expect_equal(ir@retention$samp1, c(1 / (4 + 1 + 1),
#                 0.5 / (4 + 0.5), 2 / (10 + 4 + 2)), tolerance = 0.0001)
#         expect_equal(ir@retention$samp2, c(1 / (0 + 2 + 1),
#                 0.25 / (0 + 0.25), 3 / (3 + 0 + 3)), tolerance = 0.0001)
#
#     })
#
#
# test_that('format with gene and extension intron names',
#     {
#         i2t <- data_frame(intron = c('i1', 'i1', 'i2', 'i3'),
#             target_id = c('t1', 't2', 't3', 't2'),
#             gene = c('g1', 'g1', 'g2', 'g1'),
#             intron_extension = c('i1_ext', 'i1_ext', 'i2_ext', 'i3_ext'))
#
#         targ_exp <- data_frame(
#             samp1 = c(1, 0.5, 4, 1, 0, 2),
#             samp2 = c(1, 0.25, 0, 2, 8, 3),
#             target_id = c('i1_ext', 'i2_ext', 't1', 't2', 't3', 'i3_ext')
#             )
#
#         ir <- newIntronRetention(targ_exp, i2t, factor(c('c1', 'c2')), TRUE)
#
#         expect_equal(sort(rownames(ir@numerator)), sort(unique(i2t$intron)))
#     })
#
# test_that('lowExpressionFilter',
#     {
#         i2t <- data.frame(
#             intron = c('i1', 'i2', 'i3', 'i4'),
#             target_id = c('t1', 't2', 't3', 't4'),
#             gene = c('g1', 'g1', 'g2', 'g3'),
#             intron_extension = c('i1_ext', 'i2_ext', 'i3_ext', 'i4_ext'),
#             stringsAsFactors = F)
#
#         targExp <- data.frame(
#             samp1 = c(rep(0, 4), 1:4),
#             samp2 = c(rep(0, 4), c(1, 0, 2, 3)),
#             samp3 = c(rep(0, 4), 1:4),
#             target_id = c('i1_ext', 'i2_ext', 'i3_ext', 'i4_ext',
#                 't1', 't2', 't3', 't4'),
#             stringsAsFactors = F)
#
#         ir <- newIntronRetention(targExp, i2t, factor(c('c1', 'c1', 'c2')))
#         ir <- lowExpressionFilter(ir, 0.25)
#
#         expect_equal(ir@validIntrons$c1, c(F, F, T, T))
#         expect_equal(ir@validIntrons$c2, c(F, T, T, T))
#     })
#
# test_that('retentionTest',
#     {
#         i2t <- data.frame(
#             intron = c('i1', 'i2', 'i3', 'i4'),
#             target_id = c('t1', 't2', 't3', 't4'),
#             gene = c('g1', 'g1', 'g2', 'g3'),
#             intron_extension = c('i1_ext', 'i2_ext', 'i3_ext', 'i4_ext'),
#             stringsAsFactors = F)
#
#         targExp <- data.frame(
#             samp1 = c(rep(0, 4), 1:4),
#             samp2 = c(rep(0, 4), c(1, 0, 2, 3)),
#             samp3 = c(rep(0, 4), 1:4),
#             target_id = c('i1_ext', 'i2_ext', 'i3_ext', 'i4_ext',
#                 't1', 't2', 't3', 't4'),
#             stringsAsFactors = F)
#
#         ir <- newIntronRetention(targExp, i2t, factor(c('c1', 'c1', 'c2')))
#         ir <- lowExpressionFilter(ir, 0.25)
#
#     })
#
# test_that('intron length',
#     {
#         i_names <- c('chr1:1-4', 'chr3:10-20', 'chrX:13-14')
#         lens <- intron_length(i_names)
#         expect_equal(lens, c(3, 10, 1))
#     })
# # test_that('retentionTestSingle',
# #     {
# #         set.seed(42)
# #         data.frame(
# #             samp1 = runif(10),
# #             samp2 = runif(10),
# #             samp3 = runif(10))
# #         # TODO: write me
# #     })