tests/testthat/test_drugSensitivitySig.R

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

library(PharmacoGx)
require(parallel)
context("Checking drugSensitivitySig.")

test_that("Sensitivity result did not change since last time", {
	data(GDSCsmall)

 drug.sensitivity <- drugSensitivitySig(GDSCsmall, mDataType="rna", nthread=1, features = fNames(GDSCsmall, "rna")[seq_len(50)])
	expect_equal_to_reference(drug.sensitivity@.Data, "drug.sensitivityGDSCSmall.rds")

	### TODO:: Determine why this causes 'Fatal error: length > 1 in coercion to logical' when run on Appveyor
	# Added verbose = FALSE argument to correct printing issues
	#drug.sensitivity <- drugSensitivitySig(GDSCsmall, mDataType="rna", nthread=1, features = fNames(GDSCsmall, "rna")[seq_len(50)], sensitivity.cutoff = 0.2, sensitivity.measure="auc_recomputed", verbose = FALSE)
	#expect_equal_to_reference(drug.sensitivity@.Data, "drug.sensitivity.discreteGDSCSmall.rds", tolerance = 0.2)

	drug.sensitivity <- drugSensitivitySig(GDSCsmall, mDataType="rna", nthread=1, drugs=treatmentNames(GDSCsmall)[1:2], features = fNames(GDSCsmall, "rna")[seq_len(10)], sensitivity.measure=c("auc_recomputed","auc_published"))
	expect_equal_to_reference(drug.sensitivity@.Data, "drug.sensitivity.MANOVAGDSCSmall.rds")

})