tests/testthat/test_419varpart.R

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

start <- as.POSIXlt(Sys.time())
library(pasilla)
context("419varpart.R: Does variancePartition work as expected?")

## Some changes were made to the surrogate detectors in 2017-01/2016-12.  In at least one instance
## an error crept in.  In addition, in this time frame I added a hook to the batch_counts() function
## which allows it to call on get_model_adjust() when a batch adjustment method is actually in it.
## The result is a more flexible batch method, but sadly one which has/had at least one error.
pasilla <- new.env()
load("pasilla.rda", envir = pasilla)
pasilla_expt <- pasilla[["expt"]]

pasilla_norm <- normalize_expt(pasilla_expt, filter = TRUE, transform = "log2",
                               convert = "cpm", norm = "quant")

pasilla_varpart <- sm(simple_varpart(pasilla_norm, predictor = NULL,
                                     factors = c("condition", "batch")))

## Grab the model and see if it survived.
expected <- "condition + batch"
actual <- as.character(pasilla_varpart[["model_used"]])[[2]]
test_that("Does my varpart function return a sane model?", {
  expect_equal(expected, actual)
})

## Something strange changed here.
## See if the variance by condition is as expected
##expected <- c(0.8451941, 0.8436158, 0.8364982, 0.8361348, 0.8240863, 0.8174928)
expected <-  c(0.9929197, 0.9905977, 0.9900641, 0.9890613, 0.9885474, 0.9867127)
actual <- head(pasilla_varpart[["sorted_df"]])[["condition"]]
test_that("Do we get expected values of variance by condition?", {
  expect_equal(expected, actual, tolerance = 0.01)
})

end <- as.POSIXlt(Sys.time())
elapsed <- round(x = as.numeric(end - start))
message("\nFinished 19varpart.R in ", elapsed,  " seconds.")