tests/testthat/test_TR006_DSAVEGenerateSNODataset.R

In SysBioChalmers/DSAVE-R: DSAVE: Tools to Investigate Variation and Purity of Subpopulations in Single-Cell RNA-Seq Data

test_that("TR006 - DSAVEGenerateSNODataset",{

  extrDir <- downloadData("http://cf.10xgenomics.com/samples/cell-exp/1.1.0/b_cells/b_cells_filtered_gene_bc_matrices.tar.gz", "B10k");
  dataDir = paste0(extrDir,"/filtered_matrices_mex/hg19");
  ds = Read10X(data.dir = dataDir);

  ds2 = ds[, 1:100];

  ds3 = DSAVEGenerateSNODataset(ds2);

  UMIs1 = as.vector(colSums(as.matrix(ds2)));
  UMIs2 = as.vector(colSums(as.matrix(ds3)));

  #check that the UMI distribution match
  expect_equal(UMIs1, UMIs2, info = "TR006: UMIDistr mismatch")

  #check that sparse input gives sparse output
  expect_true(is(ds2, 'sparseMatrix') & is(ds3, 'sparseMatrix'), info = "TR006: Failure on sparse input")

  #check that matrix input gives matrix output
  ds4 = as.matrix(ds2);
  ds5 = DSAVEGenerateSNODataset(ds4);
  expect_true(is.matrix(ds4) & is.matrix(ds5), info = "TR006: Failure on non-sparse input")

})