..Rcheck/tests/testthat/test-create_deltaq.R

In drake69/semseeker: Stochastic Epigenetic Mutations SEM Seeker

test_that("semeeker", {

  ssEnv <- init_env(tempFolder, parallel_strategy = "sequential")

  nitem <- 1e4
  nsamples <- 20

  probe_features <- PROBES_Gene_Whole[!is.na(PROBES_Gene_Whole$START),c("CHR","START","PROBE")]
  probe_features <- unique(probe_features)
  probe_features$END <- probe_features$START

  nitem <- min(nitem, nrow(probe_features))
  probe_features <- probe_features[probe_features$PROBE %in% sample(x=probe_features[,"PROBE"] , size=nitem),]

  methylation_data <- rnorm(nitem*nsamples,mean = 0.5, sd = 0.7)
  methylation_data <- as.data.frame(matrix(methylation_data,nitem,nsamples))

  beta_superior_thresholds <- data.frame(rnorm(nitem, mean = 1, sd=0.2))
  beta_inferior_thresholds <- data.frame(rnorm(nitem, mean=0.2, sd=0.2))

  row.names(beta_superior_thresholds) <- probe_features$PROBE
  row.names(beta_inferior_thresholds) <- probe_features$PROBE
  row.names(methylation_data) <- probe_features$PROBE

  Sample_ID <- stri_rand_strings(nsamples, 15, pattern = "[A-Za-z]")
  colnames(methylation_data) <- Sample_ID
  Sample_Group <- rep("Control",nsamples)
  sample_sheet <- data.frame(Sample_Group, Sample_ID)
  beta_medians <- beta_superior_thresholds + beta_inferior_thresholds / 2
  sliding_window_size <- 11
  bonferroni_threshold <- 0.01

  # browser()
  sp <- analyze_population(methylation_data=methylation_data,
    sliding_window_size = 11,
    sliding_window_size = sliding_window_size,
    beta_thresholds = beta_thresholds,
    sample_sheet = mySampleSheet,
    bonferroni_threshold = bonferroni_threshold,
    probe_features = probe_features,
    bonferroni_threshold = 0.01,
  )

  create_multiple_bed( sample_sheet)

  resiltPopulation <- deltaq_get( sp)

  # test deltaq creation
  tempresult_folder <- file.path(tempFolder,"Data","Control","DELTAQ_BOTH")
  fileToRead <- file_path_build(tempresult_folder, c("MULTIPLE", "DELTAQ" ,"BOTH" ), "fst")
  localFileRes_both <- fst::read_fst(fileToRead)
  testthat::expect_true(sum(is.na(localFileRes_both$VALUE))==0)

})