test_intersectPSet.R
In PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

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

# ###TO-DO:: This test takes forever to run; consider making the intersections smaller
# test_that("Intersection result did not change since last time", {
# 	data(GDSCsmall)
# 	data(CCLEsmall)
# 	common <- intersectPSet(list('GDSC'=GDSCsmall, 'CCLE'=CCLEsmall), intersectOn = c("drugs", "cell.lines","concentrations"))	
# 	expect_equal_to_reference(common, "intersectedSmallData.rds", tolerance=1e-3)
# 	expect_equal(sum(!is.na(common$CCLE@sensitivity$profiles$auc_recomputed_star)),sum(!is.na(common$CCLE@sensitivity$profiles$auc_recomputed_star)))
# 	expect_equal(drugNames(common$CCLE), drugNames(common$GDSC))
# 	expect_equal(cellNames(common$CCLE), cellNames(common$GDSC))
# })
# 
# test_that("Strict Intersection result did not change since last time", {
# 	data(GDSCsmall)
# 	data(CCLEsmall)
# 	common <- intersectPSet(list('GDSC'=GDSCsmall, 'CCLE'=CCLEsmall), intersectOn = c("drugs", "cell.lines","concentrations"), strictIntersect=TRUE)	
# 	expect_equal_to_reference(common, "intersectedSmallDataStrict.rds", tolerance=1e-3)
# 	expect_equal(sum(!is.na(common$CCLE@sensitivity$profiles$auc_recomputed_star)),sum(!is.na(common$CCLE@sensitivity$profiles$auc_recomputed_star)))
# 	expect_equal(drugNames(common$CCLE), drugNames(common$GDSC))
# 	expect_equal(cellNames(common$CCLE), cellNames(common$GDSC))
# 	expect_equal(rownames(common$GDSC@sensitivity$profiles), rownames(common$CCLE@sensitivity$profiles))
# })