tests/testthat/test_lmmTestAllRegions.R

In lissettegomez/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

# Lizhong Liu
context("lmmTestAllRegions")

data(betasChr22_df)
data(pheno_df)

CpGisland_ls <- readRDS(
  system.file ("extdata", "CpGislandsChr22_ex.RDS",
               package = 'coMethDMR',
               mustWork = TRUE
  )
)

coMeth_ls <- CoMethAllRegions(
  dnam = betasChr22_df,
  rDropThresh_num = 0.5,
  CpGs_ls = CpGisland_ls,
  arrayType = "450k",
  returnAllCpGs = FALSE
)

test_that("lmmTestAllRegions returns df with correct classes", {

  expect_s3_class(
    lmmTestAllRegions(
      betas = betasChr22_df,
      region_ls = coMeth_ls,
      pheno_df,
      contPheno_char = "stage",
      covariates_char = c("age.brain", "sex"),
      modelType = "randCoef",
      arrayType = "450k"
    ),
    "data.frame"
  )

})