tests/testthat/test-custom_files.R

In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

test_that("Tests with custom files",{
  source(system.file("ext/functions4tests.R", package = "viewpoly"))
  
  # upload custom files
  dosages <- phases <- genetic_map <- mks_pos <- list()
  dosages$datapath <- system.file("ext/dosage.tsv.gz", package = "viewpoly")
  phases$datapath <- system.file("ext/phases.tsv.gz", package = "viewpoly")
  genetic_map$datapath <- system.file("ext/map.tsv.gz", package = "viewpoly")

  viewmap_obj <- prepare_map_custom_files(dosages, phases, genetic_map)

  expect_equal(check_viewmap(viewmap_obj),0)

  check_viewmap_values(viewmap_obj,
                       c(887, 1063,543,188,54,10),
                       c(181, 640, 671, 608, 645),
                       401368.7)

  selected_mks <- qtl_info <- blups <- beta.hat <- profile <- effects <- probs <- list()
  selected_mks$datapath = system.file("ext/selected_mks.tsv.gz", package = "viewpoly")
  qtl_info$datapath = system.file("ext/qtl_info.tsv.gz", package = "viewpoly")
  blups$datapath = system.file("ext/blups.tsv.gz", package = "viewpoly")
  beta.hat$datapath = system.file("ext/beta.hat.tsv.gz", package = "viewpoly")
  profile$datapath = system.file("ext/profile.tsv.gz", package = "viewpoly")
  effects$datapath = system.file("ext/effects.tsv.gz", package = "viewpoly")
  probs$datapath = system.file("ext/probs.tsv.gz", package = "viewpoly")

  viewqtl_obj <- prepare_qtl_custom_files(selected_mks, qtl_info, blups,
                                          beta.hat, profile, effects, probs)

  expect_equal(check_viewqtl(viewqtl_obj),0)

  check_viewqtl_qtlpoly_values(viewqtl_obj,
                               245183.2,
                               6.702273,
                               3.091306e-10,
                               341.4562,
                               4.29507e-05,
                               -7.647564e-11,
                               1)

})