tests/testthat/test_tsum_statistic_on_qm.R

In bahlolab/exSTRa: Expanded STR algorithm: detecting expansions in Illumina sequencing data

context("Check internal calculation of tsum statistic")
# 

# Make a small example matrix
qm_small <- make_quantiles_matrix(exstra_wgs_pcr_2["HD", 1:4], 
  method = "quantile7")$y.mat[, c(49, 31, 99)]

test_that("make_quantiles_matrix() has consistent output",
  expect_equal(qm_small,
    structure(c(59, 57, 57.76, 50.16, 43, 44, 47.2, 33.6, 92, 80.48, 
      94.78, 80.32), .Dim = 4:3, .Dimnames = list(c("WGSrpt_02", "WGSrpt_04", 
        "WGSrpt_05", "WGSrpt_07"), NULL))
    )
)

bmu <- colMeans(qm_small)
bvar <- colMeans(qm_small ^ 2) - bmu ^ 2

test_that("qm_tsum_stat_bare_ creating the correct tsums",
  expect_equal(qm_tsum_stat_bare_(qm_small, bmu, bvar),
    c(WGSrpt_02 = 0.138386565958629, WGSrpt_04 = 0.00590495129951718, 
      WGSrpt_05 = 0.179419067436132, WGSrpt_07 = -0.323710584694278), 
    tolerance = 1e-10)
)


# Example with some quantile levels with zero variance
qm_small_0var <- make_quantiles_matrix(exstra_wgs_pcr_2["EPM1A", 2:5], 
  method = "quantile7")$y.mat[, c(49, 31, 60, 99)]

test_that("make_quantiles_matrix() has consistent output",
  expect_equal(qm_small_0var,
    structure(c(34.3529411764706, 25, 25, 25, 25, 25, 25, 25, 37, 
      25, 25, 25, 37, 37, 37, 37), .Dim = c(4L, 4L), .Dimnames = list(
        c("WGSrpt_04", "WGSrpt_05", "WGSrpt_07", "WGSrpt_08"), NULL))
  )
)

bmu <- colMeans(qm_small_0var)
bvar <- colMeans(qm_small_0var ^ 2) - bmu ^ 2

test_that("qm_tsum_stat_bare_ creating the correct tsums with some 0 variances",
  expect_equal(qm_tsum_stat_bare_(qm_small_0var, bmu, bvar),
    c(WGSrpt_04 = 0.190251572327043, WGSrpt_05 = -0.0634171907756811, 
      WGSrpt_07 = -0.0634171907756811, WGSrpt_08 = -0.0634171907756811), 
    tolerance = 1e-10)
)