tests/testthat/test-setters.R
In descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control
## Test that changing values of slots by setters is robust
file_vec <- system.file("extdata",
c("bam_files/H3K79me2_0_dm3-filtered.bam",
"bam_files/H3K79me2_0_hg19-filtered.bam",
"bigwig_files/H3K79me2_0-filtered.bw",
"bigwig_files/input_0-filtered.bw",
"bam_files/input_0_hg19-filtered.bam"),
package="ChIPSeqSpike")
file_empty <- system.file(c("extdata/empty_files/input.wig_empty.bw"),
package="ChIPSeqSpike")
e <- Experiment(endogenousBamFilePath = file_vec[2],
exogenousBamFilePath = file_vec[1],
bigWigFilePath = file_vec[3],
name = "H3K79me2_0", endoScalingFactor = 1, exoScalingFactor = 2,
endoNb = 3, exoNb = 4)
eboost <- ExperimentLoaded(endogenousBamFilePath = file_vec[2],
exogenousBamFilePath = file_vec[1],
bigWigFilePath = file_vec[3],
name = "H3K79me2_0", endoScalingFactor = 1, exoScalingFactor = 2,
endoNb = 3, exoNb = 4)
csds <- ChIPSeqSpikeDataset(endogenousBam_vec = file_vec[2],
exogenousBam_vec = file_vec[1],
bigWigFile_endogenous_vec = file_vec[3],
inputBigWigFile = file_vec[4],
inputBamFile = file_vec[5],
expnames = "H3K79me2_0", inputSF = 0.7, inputNb = 1000)
csdsboost <- ChIPSeqSpikeDatasetBoost(endogenousBam_vec = file_vec[2],
exogenousBam_vec = file_vec[1],
bigWigFile_endogenous_vec = file_vec[3],
inputBigWigFile = file_vec[4],
inputBamFile = file_vec[5],
expnames = "H3K79me2_0", inputSF = 0.7, inputNb = 1000)
## For ChIPSeqSpikeDataset object
context("Scaling factors of ChIPSeqSpikeDataset objects are changed correctly.")
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(csds) <- -2,
"object@inputScalingFactor should be a positive number or 0.")
expect_error(count(csds) <- -2,
"object@inputCount should be a positive number or 0.")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(csds) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(csds) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(csds) <- 1
count(csds) <- 3
expect_equal(getScalingFactor(csds), 1)
expect_equal(getCount(csds), 3)
})
test_that("The input bigwig file is modified correctly", {
bigWigFile(csds) <- file_vec[4]
expect_equal(getBigWigFile(csds), file_vec[4])
expect_error(bigWigFile(csds) <- file_empty,
paste0(file_empty, " should contain only one point for ",
"the extension."))
})
test_that("The plotSetArrayList is modified correctly",{
expect_error(averageBindingValues(csds) <- 3,
"SetArrayList should be of type list.")
expect_error(averageBindingValues(csds) <- list(),
"The list of binding values is empty.")
expect_error(averageBindingValues(csds) <- list(c(1,2)),
"All objects in setArray list must be of type PlotSetArray.")
})
test_that("The list of matrices is modified correctly", {
expect_error(matBindingValues(csds) <- 3,
"matBinding should be of type list.")
expect_error(matBindingValues(csds) <- list(),
"The list of binding values is empty.")
expect_error(matBindingValues(csds) <- list(c(1,2),
"All objects in matBindingValList must be of type matrix."))
})
## For ChIPSeqSpikeDatasetBoost object
if(.Platform$OS.type != 'windows') {
context("Scaling factors of ChIPSeqSpikeDatasetBoost objects are changed
correctly.")
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(csdsboost) <- -2,
"object@inputScalingFactor should be a positive number or 0.")
expect_error(count(csdsboost) <- -2,
"object@inputCount should be a positive number or 0.")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(csdsboost) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(csdsboost) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(csdsboost) <- 1
count(csdsboost) <- 3
expect_equal(getScalingFactor(csdsboost), 1)
expect_equal(getCount(csdsboost), 3)
})
test_that("The input bigwig file is modified correctly", {
bigWigFile(csdsboost) <- file_vec[4]
expect_equal(getBigWigFile(csdsboost), file_vec[4])
})
test_that("The plotSetArrayList is modified correctly",{
expect_error(averageBindingValues(csdsboost) <- 3,
"SetArrayList should be of type list.")
expect_error(averageBindingValues(csdsboost) <- list(),
"The list of binding values is empty.")
expect_error(averageBindingValues(csdsboost) <- list(c(1,2)),
"All objects in setArray list must be of type PlotSetArray.")
})
}
test_that("The list of matrices is modified correctly", {
expect_error(matBindingValues(csds) <- 3,
"matBinding should be of type list.")
expect_error(matBindingValues(csds) <- list(),
"The list of binding values is empty.")
expect_error(matBindingValues(csds) <- list(c(1,2),
"All objects in matBindingValList must be of type matrix."))
})
## For Experiment object
context("Scaling factors of Experiment objects are changed correctly.")
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(e) <- -2,
"object@endogenousScalingFactor should be a positive number or 0")
expect_error(exogenousScalingFactor(e) <- -2,
"object@exogenousScalingFactor should be a positive number or 0")
expect_error(count(e) <- -2,
"object@endoCount should be a positive number or 0")
expect_error(exoCount(e) <- -2,
"object@exoCount should be a positive number or 0")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(e) <- "toto",
"Scaling factor should be numeric.")
expect_error(exogenousScalingFactor(e) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(e) <- "toto",
"Counts should be numeric.")
expect_error(exoCount(e) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(e) <- 1
exogenousScalingFactor(e) <- 2
count(e) <- 3
exoCount(e) <- 4
expect_equal(getScalingFactor(e), 1)
expect_equal(getExogenousScalingFactor(e), 2)
expect_equal(getCount(e), 3)
expect_equal(getExoCount(e), 4)
})
test_that("The bigwig file is modified correctly", {
bigWigFile(e) <- file_vec[3]
expect_equal(getBigWigFile(e), file_vec[3])
expect_error(bigWigFile(e) <- file_empty,
paste0(file_empty, " should contain only one point for ",
"the extension."))
})
## For ExperimentLoaded object
context("Scaling factors of Experiment objects are changed correctly.")
if(.Platform$OS.type != 'windows') {
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(eboost) <- -2,
"object@endogenousScalingFactor should be a positive number or 0")
expect_error(exogenousScalingFactor(eboost) <- -2,
"object@exogenousScalingFactor should be a positive number or 0")
expect_error(count(eboost) <- -2,
"object@endoCount should be a positive number or 0")
expect_error(exoCount(eboost) <- -2,
"object@exoCount should be a positive number or 0")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(eboost) <- "toto",
"Scaling factor should be numeric.")
expect_error(exogenousScalingFactor(eboost) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(eboost) <- "toto",
"Counts should be numeric.")
expect_error(exoCount(eboost) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(eboost) <- 1
exogenousScalingFactor(eboost) <- 2
count(eboost) <- 3
exoCount(eboost) <- 4
expect_equal(getScalingFactor(eboost), 1)
expect_equal(getExogenousScalingFactor(eboost), 2)
expect_equal(getCount(eboost), 3)
expect_equal(getExoCount(eboost), 4)
})
test_that("The bigwig file is modified correctly", {
bigWigFile(eboost) <- file_vec[3]
expect_equal(getBigWigFile(eboost), file_vec[3])
})
}
descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.
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## Test that changing values of slots by setters is robust
file_vec <- system.file("extdata",
c("bam_files/H3K79me2_0_dm3-filtered.bam",
"bam_files/H3K79me2_0_hg19-filtered.bam",
"bigwig_files/H3K79me2_0-filtered.bw",
"bigwig_files/input_0-filtered.bw",
"bam_files/input_0_hg19-filtered.bam"),
package="ChIPSeqSpike")
file_empty <- system.file(c("extdata/empty_files/input.wig_empty.bw"),
package="ChIPSeqSpike")
e <- Experiment(endogenousBamFilePath = file_vec[2],
exogenousBamFilePath = file_vec[1],
bigWigFilePath = file_vec[3],
name = "H3K79me2_0", endoScalingFactor = 1, exoScalingFactor = 2,
endoNb = 3, exoNb = 4)
eboost <- ExperimentLoaded(endogenousBamFilePath = file_vec[2],
exogenousBamFilePath = file_vec[1],
bigWigFilePath = file_vec[3],
name = "H3K79me2_0", endoScalingFactor = 1, exoScalingFactor = 2,
endoNb = 3, exoNb = 4)
csds <- ChIPSeqSpikeDataset(endogenousBam_vec = file_vec[2],
exogenousBam_vec = file_vec[1],
bigWigFile_endogenous_vec = file_vec[3],
inputBigWigFile = file_vec[4],
inputBamFile = file_vec[5],
expnames = "H3K79me2_0", inputSF = 0.7, inputNb = 1000)
csdsboost <- ChIPSeqSpikeDatasetBoost(endogenousBam_vec = file_vec[2],
exogenousBam_vec = file_vec[1],
bigWigFile_endogenous_vec = file_vec[3],
inputBigWigFile = file_vec[4],
inputBamFile = file_vec[5],
expnames = "H3K79me2_0", inputSF = 0.7, inputNb = 1000)
## For ChIPSeqSpikeDataset object
context("Scaling factors of ChIPSeqSpikeDataset objects are changed correctly.")
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(csds) <- -2,
"object@inputScalingFactor should be a positive number or 0.")
expect_error(count(csds) <- -2,
"object@inputCount should be a positive number or 0.")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(csds) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(csds) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(csds) <- 1
count(csds) <- 3
expect_equal(getScalingFactor(csds), 1)
expect_equal(getCount(csds), 3)
})
test_that("The input bigwig file is modified correctly", {
bigWigFile(csds) <- file_vec[4]
expect_equal(getBigWigFile(csds), file_vec[4])
expect_error(bigWigFile(csds) <- file_empty,
paste0(file_empty, " should contain only one point for ",
"the extension."))
})
test_that("The plotSetArrayList is modified correctly",{
expect_error(averageBindingValues(csds) <- 3,
"SetArrayList should be of type list.")
expect_error(averageBindingValues(csds) <- list(),
"The list of binding values is empty.")
expect_error(averageBindingValues(csds) <- list(c(1,2)),
"All objects in setArray list must be of type PlotSetArray.")
})
test_that("The list of matrices is modified correctly", {
expect_error(matBindingValues(csds) <- 3,
"matBinding should be of type list.")
expect_error(matBindingValues(csds) <- list(),
"The list of binding values is empty.")
expect_error(matBindingValues(csds) <- list(c(1,2),
"All objects in matBindingValList must be of type matrix."))
})
## For ChIPSeqSpikeDatasetBoost object
if(.Platform$OS.type != 'windows') {
context("Scaling factors of ChIPSeqSpikeDatasetBoost objects are changed
correctly.")
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(csdsboost) <- -2,
"object@inputScalingFactor should be a positive number or 0.")
expect_error(count(csdsboost) <- -2,
"object@inputCount should be a positive number or 0.")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(csdsboost) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(csdsboost) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(csdsboost) <- 1
count(csdsboost) <- 3
expect_equal(getScalingFactor(csdsboost), 1)
expect_equal(getCount(csdsboost), 3)
})
test_that("The input bigwig file is modified correctly", {
bigWigFile(csdsboost) <- file_vec[4]
expect_equal(getBigWigFile(csdsboost), file_vec[4])
})
test_that("The plotSetArrayList is modified correctly",{
expect_error(averageBindingValues(csdsboost) <- 3,
"SetArrayList should be of type list.")
expect_error(averageBindingValues(csdsboost) <- list(),
"The list of binding values is empty.")
expect_error(averageBindingValues(csdsboost) <- list(c(1,2)),
"All objects in setArray list must be of type PlotSetArray.")
})
}
test_that("The list of matrices is modified correctly", {
expect_error(matBindingValues(csds) <- 3,
"matBinding should be of type list.")
expect_error(matBindingValues(csds) <- list(),
"The list of binding values is empty.")
expect_error(matBindingValues(csds) <- list(c(1,2),
"All objects in matBindingValList must be of type matrix."))
})
## For Experiment object
context("Scaling factors of Experiment objects are changed correctly.")
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(e) <- -2,
"object@endogenousScalingFactor should be a positive number or 0")
expect_error(exogenousScalingFactor(e) <- -2,
"object@exogenousScalingFactor should be a positive number or 0")
expect_error(count(e) <- -2,
"object@endoCount should be a positive number or 0")
expect_error(exoCount(e) <- -2,
"object@exoCount should be a positive number or 0")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(e) <- "toto",
"Scaling factor should be numeric.")
expect_error(exogenousScalingFactor(e) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(e) <- "toto",
"Counts should be numeric.")
expect_error(exoCount(e) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(e) <- 1
exogenousScalingFactor(e) <- 2
count(e) <- 3
exoCount(e) <- 4
expect_equal(getScalingFactor(e), 1)
expect_equal(getExogenousScalingFactor(e), 2)
expect_equal(getCount(e), 3)
expect_equal(getExoCount(e), 4)
})
test_that("The bigwig file is modified correctly", {
bigWigFile(e) <- file_vec[3]
expect_equal(getBigWigFile(e), file_vec[3])
expect_error(bigWigFile(e) <- file_empty,
paste0(file_empty, " should contain only one point for ",
"the extension."))
})
## For ExperimentLoaded object
context("Scaling factors of Experiment objects are changed correctly.")
if(.Platform$OS.type != 'windows') {
test_that("Negative value cannot be given as scaling factor or count", {
expect_error(scalingFactor(eboost) <- -2,
"object@endogenousScalingFactor should be a positive number or 0")
expect_error(exogenousScalingFactor(eboost) <- -2,
"object@exogenousScalingFactor should be a positive number or 0")
expect_error(count(eboost) <- -2,
"object@endoCount should be a positive number or 0")
expect_error(exoCount(eboost) <- -2,
"object@exoCount should be a positive number or 0")
})
test_that("Non numeric value is not accepted as scaling factor or count",{
expect_error(scalingFactor(eboost) <- "toto",
"Scaling factor should be numeric.")
expect_error(exogenousScalingFactor(eboost) <- "toto",
"Scaling factor should be numeric.")
expect_error(count(eboost) <- "toto",
"Counts should be numeric.")
expect_error(exoCount(eboost) <- "toto",
"Counts should be numeric.")
})
test_that("Slot is correctly modified if a valid score is given", {
scalingFactor(eboost) <- 1
exogenousScalingFactor(eboost) <- 2
count(eboost) <- 3
exoCount(eboost) <- 4
expect_equal(getScalingFactor(eboost), 1)
expect_equal(getExogenousScalingFactor(eboost), 2)
expect_equal(getCount(eboost), 3)
expect_equal(getExoCount(eboost), 4)
})
test_that("The bigwig file is modified correctly", {
bigWigFile(eboost) <- file_vec[3]
expect_equal(getBigWigFile(eboost), file_vec[3])
})
}
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