test_that("chemical class enrichment data is returned correctly, ChemicalClassEnrichment", {
metabolites.of.interest<- c('hmdb:HMDB0000056',
'hmdb:HMDB0000439',
'hmdb:HMDB0000479',
'hmdb:HMDB0000532',
'hmdb:HMDB0011211')
chemical.classes<-chemicalClassSurvey(db = rampDB, mets = metabolites.of.interest, background="NULL", background_type="database")
enrichedClassSets <- chemicalClassEnrichment(db = rampDB, mets = metabolites.of.interest, background="NULL", background_type="database")
expect_true(
NROW(enrichedClassSets)!=0
)
expect_true(
!is.null(enrichedClassSets))
})
test_that("chemical class enrichment data is returned correctly, ChemicalClassEnrichment, where background is Saliva and inferIdMapping is FALSE", {
metabolites.of.interest<- c('hmdb:HMDB0000056',
'hmdb:HMDB0000439',
'hmdb:HMDB0000479',
'hmdb:HMDB0000532',
'hmdb:HMDB0011211')
chemical.classes<-chemicalClassSurvey(db = rampDB, mets = metabolites.of.interest, background="NULL", background_type="database")
enrichedClassSets <- chemicalClassEnrichment(db = rampDB, mets = metabolites.of.interest, background="Saliva", background_type="biospecimen", inferIdMapping = F)
expect_true(
NROW(enrichedClassSets)!=0
)
expect_true(
!is.null(enrichedClassSets))
})
test_that("chemical class enrichment data is returned correctly when selecting for specific chemical classes, ChemicalClassEnrichment", {
metabolites.of.interest<- c('hmdb:HMDB0000056',
'hmdb:HMDB0000439',
'hmdb:HMDB0034365',
'hmdb:HMDB0035227',
'hmdb:HMDB0008057',
'hmdb:HMDB0011211')
chemical.classes<-chemicalClassSurvey(db = rampDB, mets = metabolites.of.interest, background="NULL", background_type="database")
enrichedClassSets <- chemicalClassEnrichment(db = rampDB, mets = metabolites.of.interest, background="NULL", background_type="database")
classy_fire_classes <- enrichedClassSets$ClassyFire_class
expect_true(
NROW(classy_fire_classes)!=0
)
expect_true(
!is.null(classy_fire_classes))
})
test_that("chemical class enrichment data is returned correctly when selecting biospecimen background for Urine metabolites", {
metabolites.of.interest<- c('hmdb:HMDB0000056',
'hmdb:HMDB0000439',
'hmdb:HMDB0034365',
'hmdb:HMDB0035227',
'hmdb:HMDB0008057',
'hmdb:HMDB0011211')
chemical.classes<-chemicalClassSurvey(db = rampDB, mets = metabolites.of.interest, background="Urine", background_type="biospecimen")
enrichedClassSets <- chemicalClassEnrichment(db = rampDB, mets = metabolites.of.interest, background="Urine", background_type="biospecimen")
classy_fire_classes <- enrichedClassSets$ClassyFire_class
expect_true(
NROW(classy_fire_classes)!=0
)
expect_true(
!is.null(classy_fire_classes))
})
test_that("chemical class enrichment data is returned correctly when performing enrichment used inferIdMapping = T", {
metabolites.of.interest<- c('hmdb:HMDB0000056',
'hmdb:HMDB0000439',
'hmdb:HMDB0034365',
'hmdb:HMDB0035227',
'hmdb:HMDB0008057',
'hmdb:HMDB0011211')
chemical.classes<-chemicalClassSurvey(db = rampDB, mets = metabolites.of.interest, background_type="database", inferIdMapping = T)
enrichedClassSets <- chemicalClassEnrichment(db = rampDB, mets = metabolites.of.interest, background_type="database", inferIdMapping = T)
classy_fire_classes <- enrichedClassSets$ClassyFire_class
expect_true(
NROW(classy_fire_classes)!=0
)
expect_true(
!is.null(classy_fire_classes))
})
test_that("chemical class enrichment data is returned correctly when performing enrichment used inferIdMapping = T, and biospecimen background, Urine", {
metabolites.of.interest<- c('hmdb:HMDB0000056',
'hmdb:HMDB0000439',
'hmdb:HMDB0034365',
'hmdb:HMDB0035227',
'hmdb:HMDB0008057',
'hmdb:HMDB0011211')
chemical.classes<-chemicalClassSurvey(db = rampDB, mets = metabolites.of.interest, background_type="database", inferIdMapping = T)
enrichedClassSets <- chemicalClassEnrichment(db = rampDB, mets = metabolites.of.interest, background = 'Urine', background_type="biospecimen", inferIdMapping = T)
classy_fire_classes <- enrichedClassSets$ClassyFire_class
expect_true(
NROW(classy_fire_classes)!=0
)
expect_true(
!is.null(classy_fire_classes))
})
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