tests/testthat/test-subsetting.R

In OmicFlow: Fast and Efficient (Automated) Analysis of Sparse Omics Data

test_that("Testing subsetting of data", {
  taxa <- metagenomics$new(
    biomData = "input/metagenomics/biom_with_taxonomy_hdf5.biom",
    metaData = "input/metagenomics/metadata.tsv",
    treeData = "input/metagenomics/rooted_tree.newick"
  )
  
  # Perform feature subset
  taxa$feature_subset(Kingdom == "Bacteria")
  expect_snapshot(taxa)
  
  # In between reset
  taxa$reset()
  
  # Perform metadata subset
  taxa$sample_subset(treatment == "tumor")
  expect_snapshot(taxa)
})