tests/testthat/test_AESPCA_pVals.R

In pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

context("AESPCA_pVals")

data("colonSurv_df")
data("colon_pathwayCollection")

test_that("AESPCA_pVals gives correct class results", {
  
  colon_OmicsSurv <- CreateOmics(
    assayData_df = colonSurv_df[, -(2:3)],
    pathwayCollection_ls = colon_pathwayCollection,
    response = colonSurv_df[, 1:3],
    respType = "surv"
  )
  
  #aespca
  expect_s3_class(AESPCA_pVals(
    object = colon_OmicsSurv,
    numPCs = 1,
    numReps = 0,
    parallel = TRUE,
    numCores = 2,
    adjustment = "BY"
  ), class = "aespcOut")
  
  # # Regular PCA
  # expect_s3_class(AESPCA_pVals(
  #   object = colon_OmicsSurv,
  #   numPCs = 1,
  #   numReps = 0,
  #   parallel = TRUE,
  #   numCores = 2,
  #   asPCA = TRUE,
  #   adjustment = "BY"
  # ), class = "aespcOut")
  
  
})