Nothing
library(Chicago)
data("cdUnitTest")
##modifications to cdUnitTest, ensuring it uses correct design directory
designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir,
settings = list(brownianNoise.samples=1, brownianNoise.subset=NA))
setkey(cdUnitTest@x, baitID, otherEndID)
context("Recalculate cdUnitTest columns")
# normaliseBaits ##Not expected to be recapitulated
# normaliseOtherEnds ##Not expected to be recapitulated
# estimateTechnicalNoise ##Not expected to be recapitulated
# estimateDistFun ## Not expected to be recapitulated
# estimateBrownianNoise
test_that("estimateBrownianNoise reproduces cdUnitTest data", {
cdRecalc <- copyCD(cdUnitTest)
cdRecalc <- estimateBrownianNoise(cdRecalc)
setkey(cdRecalc@x, baitID, otherEndID)
expect_equal(cdUnitTest@x$Bmean, cdRecalc@x$Bmean)
})
# getPvals
test_that("getPvals reproduces cdUnitTest data", {
cdRecalc <- copyCD(cdUnitTest)
cdRecalc <- getPvals(cdRecalc)
setkey(cdRecalc@x, baitID, otherEndID)
expect_equal(cdUnitTest@x$log.p, cdRecalc@x$log.p)
})
# getScores
test_that("getScores reproduces cdUnitTest data", {
cdRecalc <- copyCD(cdUnitTest)
cdRecalc <- getScores(cdRecalc)
setkey(cdRecalc@x, baitID, otherEndID)
expect_equal(cdUnitTest@x$score, cdRecalc@x$score)
})
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