tests/testthat/test_155normalize_convert.R

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

start <- as.POSIXlt(Sys.time())
context("155normalize_convert.R")
## 2018-04, exported functions in normalize_convert:
## convert_counts(), divide_seq(), hpgl_rpkm()

pombe_expt <- make_pombe_expt()

## I will mostly access these functions from normalize_expt, so first invoke them from there.
testing <- normalize_expt(pombe_expt, convert = "cpm")
test_counts <- exprs(testing)

test_genes <- c("SPAC212.11", "SPAC212.09c", "SPNCRNA.70", "SPAC212.12", "SPAC212.04c",
                "SPAC212.03", "SPAC212.02", "SPAC212.01c", "SPAC977.03", "SPAC977.04")

expected <- c(0.51068105, 1.46820803, 0.00000000, 0.06383513, 2.36189987,
              0.00000000, 0.00000000, 0.12767026, 0.00000000, 0.00000000)
names(expected) <- test_genes
actual <- test_counts[test_genes, 1]
test_that("cpm modification provides expected values?", {
  expect_equal(expected, actual, tolerance = 0.0001)
})

testing <- normalize_expt(pombe_expt, convert = "rpkm", column = "cds_length")
test_counts <- exprs(testing)
expected <- c(0.09019446, NA, NA, 0.17159982, 2.72422131,
              0.00000000, 0.00000000, 0.15144752, 0.00000000, 0.00000000)
names(expected) <- test_genes
actual <- test_counts[test_genes, 1]
test_that("rpkm modification provides expected values?", {
  expect_equal(expected, actual, tolerance = 0.0001)
})

## Since I do not seem to have a usable fission BSgenome, I would ask the reader to
## look to ../travis/test_11norm_convert.R for the test of convert_counts()
## using pasilla_expt and the method 'cp_seq_m'.

end <- as.POSIXlt(Sys.time())
elapsed <- round(x = as.numeric(end - start))
message("\nFinished 155normalize_convert.R in ", elapsed,  " seconds.")