tests/testthat/test-standardize.R

In scMerge: scMerge: Merging multiple batches of scRNA-seq data

context("Test-standardize function")
set.seed(1234)
L = ruvSimulate(m = 500, n = 2000, nc = 100, nCelltypes = 3, nBatch = 2, lambda = 0.1, sce = FALSE)
Y = t(log2(L$Y + 1L)); M = L$M; ctl = L$ctl; batch = L$batch;

s1 = standardize(Y, batch)
s2 = standardize2(Y, batch)


expect_equal(s1$s.data, 
             s2$stand_Y, tol = 1e-6)

expect_equal(s1$stand.mean[,1], 
             unname(s2$stand_mean), tol = 1e-6)

# expect_equal(unname(s1$stand.var), 
#              unname(s2$stand.var), tol = 1e-6)

# Y_da = as(Y, "HDF5Array")
# s3 = standardize2(Y_da, batch)
# s1$s.data[1:5,1:5]
# s3$s.data[1:5,1:5]