/
test-fitPoisBG.R
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test-fitPoisBG.R
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# specs:
# When groupvar is not provided,
# - the function outputs a GeoMx S4 class with length same as length of negative probes, featfact, in featureData. The value is NA for non-negative probes.
# - If size_scale="first", sizefact[1]=1
# - If size_scale="sum", sum(sizefact)=1
# load example data:
data("demoData")
# run function:
res <- fitPoisBG(demoData, size_scale = "first")
## test basic structure:
# spec: "The function outputs a GeoMx S4 class with length same as length of ROIs, sizefact, in phenoData.
# The value is NA for non-negative probes."
test_that("fitPoisBG returns a well-formatted geomxset object", {
expect_true(class(res) == "NanoStringGeoMxSet")
expect_true(nrow(phenoData(res)) == nrow(phenoData(demoData)))
expect_true(nrow(featureData(res)) == nrow(featureData(demoData)))
# 1 The function outputs a GeoMx S4 class with length same as length of ROIs, sizefact, in phenoData.
expect_true("sizefact" %in% varLabels(res))
expect_false(any(is.na(res[["sizefact"]])))
# 2 The function outputs a GeoMx S4 class with length same as length of negative probes, featfact, in featureData. The value is NA for non-negative probes
expect_true(all(is.na(fData(res)$featfact[fData(res)$featfact == "Endogenous"])))
expect_identical(!is.na(fData(res)$featfact), fData(res)$CodeClass == "Negative")
})
## test size factors are correct:
test_that("sizefact is correct", {
# Spec 3: If size_scale="first", sizefact[1]=1
res <- fitPoisBG(demoData, size_scale = "first")
expect_equal(pData(res)$sizefact[1], 1, tol = 1e-5)
# Spec 4: If size_scale="sum", sum(sizefact)=1
res <- fitPoisBG(demoData, size_scale = "sum")
expect_equal(sum(pData(res)$sizefact), 1, tol = 1e-5)
})
## test that values haven't changed from June 2021 initial release:
test_that("fitPoisBG is stable", {
res <- fitPoisBG(demoData, size_scale = "sum")
expect_equal(pData(res)$sizefact[c(1, 10, 50)], c(0.011925349, 0.013114282, 0.007818129), tol = 1e-5)
expect_equal(fData(res)$featfact[c(7932, 7933, 7934)], c(319, 380, 299), tol = 1e-2)
})
# specs
# When groupvar is provided but not found in the phenodata,
# 1. The function returns an error saying this groupvar is not found in the S4 object.
# load example data:
res <- fitPoisBG(demoData, size_scale = "first")
test_that("The function returns an error", {
expect_error(
fitPoisBG(demoData, size_scale = "first", groupvar = "slidename"),
"is not found in the S4 object"
)
})
# specs
# When groupvar is provided and found in the phenodata, but the it only has one unique value,
# 1. The function returns a warning message saying that the groupvar has only one value
# load example data:
res <- fitPoisBG(demoData, size_scale = "first")
test_that("The function returns a warning messag", {
expect_warning(
fitPoisBG(demoData, size_scale = "first", groupvar = "segment"),
"has only one value"
)
})
# specs:
# When groupvar is provided and found in the phenodata with more than one unique value,
# 1 When groupvar is provided, the function outputs a GeoMx S4 class with length same as length of ROIs, sizefact, in phenoData.
# 2 The function outputs a GeoMx S4 class with length same as length of negative probes, featfact, in featureData.
# The value is NA for non-negative probes.
# 3 If size_scale="first", sizefact[1]=1
# 4 If size_scale="sum", sum(sizefact)=1
# load example data:
res <- fitPoisBG(demoData, size_scale = "first")
# run function:
res <- fitPoisBG(demoData, size_scale = "first", groupvar = "slide name")
## test basic structure:
# - The function outputs a GeoMx S4 class with length same as length of ROIs, sizefact, in phenoData.
# - The function outputs a GeoMx S4 class with length same as length of negative probes, featfact, in featureData for each unique slide value.
# - the group variable name for slide id of ROIs in experimentData: fitPoisBG_sp_var
test_that("fitPoisBG returns a well-formatted geomxset object", {
expect_true(class(res) == "NanoStringGeoMxSet")
# 1 The function outputs a GeoMx S4 class with length same as length of ROIs, sizefact, in phenoData
expect_true(nrow(phenoData(res)) == nrow(phenoData(demoData)))
expect_true(nrow(featureData(res)) == nrow(featureData(demoData)))
expect_true(all(is.na(fData(res)$featfact[fData(res)$featfact != "Negative"])))
# 2 The function outputs a GeoMx S4 class with length same as length of negative probes, featfact, in featureData.
# The value is NA for non-negative probes.
for (i in grep("featfact_", fvarLabels(res))) {
expect_identical(!is.na(fData(res)[, i]), fData(res)$CodeClass == "Negative")
}
expect_identical(
fvarLabels(res)[grep("featfact_", fvarLabels(res))],
paste0("featfact_", unique(demoData[["slide name"]]))
)
expect_equal(notes(res)$fitPoisBG_sp_var, "slide name")
})
## test size factors are correct:
test_that("sizefact is correct", {
# 3 Spec: If size_scale="first", sizefact[1]=1
res <- fitPoisBG(demoData, size_scale = "first", groupvar = "slide name")
expect_equal(pData(res)$sizefact[1], 1, tol = 1e-5)
# 4 Spec: If size_scale="sum", sum(sizefact)=1
res <- fitPoisBG(demoData, size_scale = "sum", groupvar = "slide name")
expect_equal(sum(pData(res)$sizefact), 1, tol = 1e-5)
})
## test that values haven't changed from June 2021 initial release:
test_that("fitPoisBG is stable", {
res <- fitPoisBG(demoData, size_scale = "sum", groupvar = "slide name")
expect_equal(pData(res)$sizefact[c(1, 10, 50)], c(0.011925349, 0.013114282, 0.007818129), tol = 1e-5)
expect_equal(fData(res)$"featfact_6panel-old-slide1 (PTL-10891)"[c(7932:7934)], c(313.8457, 438.5242, 356.8383), tol = 1e-2)
})