tests/testthat/test-fitZig.R

In metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

################################################################################
# metagenomeSeq plot functions unit tests
################################################################################
context("Testing fitZig")
library("metagenomeSeq"); library("testthat");


test_that("`fitZig` function provides expected values prior to split", {
  # uses the lung data and pre-calculated fitZig result from 
  # prior to this separation
  data(lungData)
  path = system.file("extdata", package = "metagenomeSeq")
  fit  = readRDS(file.path(path,"lungfit.rds"))
  
  # run the same fit
  k = grep("Extraction.Control",pData(lungData)$SampleType)
  lungTrim = lungData[,-k]
  k = which(rowSums(MRcounts(lungTrim)>0)<30)
  lungTrim = cumNorm(lungTrim)
  lungTrim = lungTrim[-k,]
  smokingStatus = pData(lungTrim)$SmokingStatus
  mod = model.matrix(~smokingStatus)
  settings = zigControl(maxit=1,verbose=FALSE)
  fit2 = fitZig(obj = lungTrim,mod=mod,control=settings)
  # because the ordering is wrong
  expect_failure(expect_equal(fit,fit2))
  # check that they're equal now 
  #fit2 = fit2[names(fit)] # old way
  setAs("fitZigResults", "list", function(from) {
    list(call = from@call, fit = from@fit, countResiduals = from@countResiduals, 
         z = from@z, eb = from@eb, taxa = from@taxa, counts = from@counts, zeroMod = from@zeroMod, 
         stillActive = from@stillActive, stillActiveNLL = from@stillActiveNLL, zeroCoef = from@zeroCoef, 
         dupcor = from@dupcor) }) # new way
  fit2 = as(fit2, "list")
  expect_equal(fit,fit2)
})

test_that("`fitZig` function treats a matrix the same", {
  # uses the lung data and pre-calculated fitZig result from 
  # prior to this separation
  data(lungData)
  path = system.file("extdata", package = "metagenomeSeq")
  fit  = readRDS(file.path(path,"lungfit.rds"))
  
  # run the same fit
  k = grep("Extraction.Control",pData(lungData)$SampleType)
  lungTrim = lungData[,-k]
  k = which(rowSums(MRcounts(lungTrim)>0)<30)
  lungTrim = cumNorm(lungTrim)
  lungTrim = lungTrim[-k,]
  smokingStatus = pData(lungTrim)$SmokingStatus
  scalingFactor = log2(normFactors(lungTrim)/1000 +1)
  mod = model.matrix(~smokingStatus)
  mod = cbind(mod,scalingFactor)
  settings = zigControl(maxit=1,verbose=FALSE)
  cnts = MRcounts(lungTrim)
  fit2 = fitZig(obj = lungTrim,mod=mod,control=settings,useCSSoffset=FALSE)
  #fit2 = fit2[names(fit)] # old way
  # new way - turning fitZigResults back to list
  fit2 = as(fit2, "list")

  # expecting failure because of call
  expect_failure(expect_equal(fit,fit2))
  fit2$call = "123"
  fit$call = "123"
  # check that they're equal
  expect_equal(fit,fit2)
})