testthat_itemselect.R
In DRomics: Dose Response for Omics

test_that("itemselect works as expected on the number of selected probes", {
  skip_on_cran()
  skip_on_os(c("mac", "linux"))
  withr::local_seed(123)
  
  ###### transcripto_sample.txt ######
  ####################################
  datafilename <- system.file("extdata", "transcripto_sample.txt", package="DRomics")
  o <- microarraydata(datafilename, check = TRUE, norm.method = "cyclicloess")
  
  s_quad0p001 <- itemselect(o, select.method = "quadratic", FDR = 0.001)
  expect_equal(length(s_quad0p001$selectindex), 80)
  
  s_quad0p05 <- itemselect(o, select.method = "quadratic", FDR = 0.05)
  expect_equal(length(s_quad0p05$selectindex), 302)
  
  s_lin0p001 <- itemselect(o, select.method = "linear", FDR = 0.001)
  expect_equal(length(s_lin0p001$selectindex), 15)
  
  s_lin0p05 <- itemselect(o, select.method = "linear", FDR = 0.05)
  expect_equal(length(s_lin0p05$selectindex), 99)
  
  s_ANOVA0p001 <- itemselect(o, select.method = "ANOVA", FDR = 0.001)
  expect_equal(length(s_ANOVA0p001$selectindex), 53)
  
  s_ANOVA0p05 <- itemselect(o, select.method = "ANOVA", FDR = 0.05)
  expect_equal(length(s_ANOVA0p05$selectindex), 198)
  
  
  ###### metabolo_sample.txt #########
  ####################################
  datafilename.m <- system.file("extdata", "metabolo_sample.txt", package="DRomics")
  o.m <- continuousomicdata(datafilename.m, check = TRUE)
  
  s_quad0p05.m <- itemselect(o.m, select.method = "quadratic", FDR = 0.05)
  expect_equal(length(s_quad0p05.m$selectindex), 36)
  
  s_quad0p05.mb <- itemselect(o.m, select.method = "quadratic", FDR = 0.05, max.ties.prop = 0.5)
  expect_equal(length(s_quad0p05.mb$selectindex), 40)
  
  
  ###### RNAseq_sample.txt ###########
  ####################################
  datafilename.r <- system.file("extdata", "RNAseq_sample.txt", package="DRomics")
  o.r <- RNAseqdata(datafilename.r, check = TRUE, transfo.method = "rlog")
  s_quad.r <- itemselect(o.r, select.method = "quadratic", FDR = 0.05)
  expect_equal(length(s_quad.r$selectindex), 43)
})