tests/testthat/test-quant.R

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

test_that("test optimisation of quantification works", 
{
  data(chr22_anno)
  data(rpfs)
  data(offsets_df)
  data(ms_df)

  psites <- get_psite_gr(rpfs, offsets_df, chr22_anno)
  # now, use Stan to estimate normalized p-site densities for our data
  ritpms <- get_ritpms(psites, chr22_anno)
  # and get these at the gene level (ignoring uORFs)
  gritpms <- gene_level_expr(ritpms, chr22_anno)
  # compare these to mass spec data
  gritpms <- gritpms %>% mutate_at("gene_id", str_replace, "\\.\\d+$", "")
  compdf <- ms_df %>%
    left_join(gritpms) %>%
    filter(is.finite(log2(expr))) %>%
    filter(ribo > 0)
  expect_true(nrow(compdf) == 39)
  expect_true(cor(compdf$ribo, log2(compdf$expr)) > 0.66)


  ftests <- ftest_orfs(psites %>% head(10000), chr22_anno, n_cores=1)
  expect_equal(colnames(ftests), c("orf_id", "spec_coef", "p.value"))
}
)