tests/testthat/test-statistic-fgsea.R

In saezlab/decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data

library(decoupleR)

# Directories -------------------------------------------------------------

# Inputs
input_dir <- system.file("testdata", "inputs", package = "decoupleR")

# Outputs
expected_dir <- system.file("testdata", "outputs", "fgsea", package = "decoupleR")

# Data to run -------------------------------------------------------------

mat <- file.path(input_dir, "mat.rds") %>%
  readRDS()

net <- file.path(input_dir, "net.rds") %>%
  readRDS()

# Test for run_fgsea function ---------------------------------------------

test_that("test run_fgsea", {
  res_1 <- run_fgsea(mat, net, minsize=0, nproc=1)
  exp_1 <- file.path(expected_dir, "output-fgsea.rds") %>%
    readRDS()

  expect_equal(res_1, exp_1, tolerance=0.01)
})