context("GeneEffect")
test_that("All datasets", {
datasets <- eval(formals(GeneEffect)[["dataset"]])
for (dataset in datasets) {
object <- GeneEffect(dataset = dataset)
expect_s4_class(object, "GeneEffect")
}
})
test_that("CRISPR : depmap_public_21q2", {
dataset <- "depmap_public_21q2"
object <- GeneEffect(dataset = dataset)
expect_s4_class(object, "GeneEffect")
expect_identical(
object = head(colnames(object), n = 3L),
expected = c("ACH_000001", "ACH_000004", "ACH_000005")
)
expect_identical(
object = head(rownames(object), n = 3L),
expected = c("A1BG_1", "A1CF_29974", "A2M_2")
)
expect_identical(
object = assayNames(object),
expected = c("effect", "probability")
)
## nolint start
expect_equal(
object = colData(object)["ACH_000004", ],
expected = DataFrame(
"achillesNReplicates" = 2,
"age" = 30,
"alias" = NA_character_,
"cas9Activity" = 52.4,
"ccleName" = "HEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE",
"cellLineName" = "HEL",
"cellLineNnmd" = -3.079202, # NOTE causes `identical()` to fail.
"cosmicid"= 907053,
"cultureMedium" = "RPMI + 10% FBS",
"cultureType" = "Suspension",
"depMapId" = "ACH-000004",
"depmapPublicComments" = NA_character_,
"lineage" = "blood",
"lineageMolecularSubtype" = NA_character_,
"lineageSubSubtype" = "M6",
"lineageSubtype" = "AML",
"primaryDisease" = "Leukemia",
"primaryOrMetastasis" = NA_character_,
"rrid" = "CVCL_0001",
"sampleCollectionSite" = "haematopoietic_and_lymphoid_tissue",
"sangerModelId" = "SIDM00594",
"sex" = "Male",
"source" = "DSMZ",
"strippedCellLineName" = "HEL",
"subtype" = paste(
"Acute Myelogenous Leukemia (AML),",
"M6 (Erythroleukemia)"
),
"wtsiMasterCellId" = 783,
row.names = "ACH_000004"
)
)
## nolint end
rowData <- rowData(object)["A1BG_1", , drop = FALSE]
rowData <- decode(rowData)
metadata(rowData) <- list()
attr(class(rowData[["dbXrefs"]]), "package") <- "IRanges"
attr(class(rowData[["geneSynonyms"]]), "package") <- "IRanges"
attr(class(rowData[["otherDesignations"]]), "package") <- "IRanges"
expect_equal(
object = rowData,
expected = DataFrame(
"chromosome" = "19",
"dbXrefs" = CharacterList(c(
"Ensembl:ENSG00000121410",
"HGNC:HGNC:5",
"MIM:138670"
)),
"description" = "alpha-1-B glycoprotein",
"featureType" = NA_character_,
"geneId" = 1L,
"geneName" = "A1BG",
"geneSynonyms" = CharacterList(c(
"A1B", "ABG", "GAB", "HYST2477"
)),
"mapLocation" = "19q13.43",
"modificationDate" = 20210518, # nolint
"nomenclatureStatus" = "O",
"otherDesignations" = CharacterList(c(
"alpha-1B-glycoprotein",
"epididymis secretory sperm binding protein Li 163pA",
"HEL-S-163pA"
)),
"typeOfGene" = "protein-coding",
"xTaxId" = 9606, # nolint
row.names = "A1BG_1"
)
)
expect_identical(
object = metadata(object)[["dataset"]],
expected = dataset
)
expect_true(
isSubset(
x = c(
"AKAP2_11217",
"C10orf113_387638",
"C12orf74_338809",
"C17orf47_284083",
"CRIPAK_285464",
"KIAA1107_23285",
"MICALCL_84953",
"PALM2_114299"
),
y = metadata(object)[["retiredGenes"]]
)
)
})
test_that("RNAi : demeter2_data_v6", {
dataset <- "demeter2_data_v6"
object <- GeneEffect(dataset = dataset)
expect_s4_class(object, "GeneEffect")
expect_identical(
object = head(colnames(object), n = 3L),
expected = c(
"A101D_SKIN",
"A1207_CENTRAL_NERVOUS_SYSTEM",
"A172_CENTRAL_NERVOUS_SYSTEM"
)
)
expect_identical(
object = head(rownames(object), n = 3L),
expected = c("A1BG_1", "A1CF_29974", "A2M_2")
)
expect_identical(
object = assayNames(object),
expected = "effect"
)
expect_identical(
object = colData(object)["A101D_SKIN", ],
expected = DataFrame(
"ccleId" = "A101D_SKIN",
"cellLineName" = "A101D",
"disease" = "skin",
"diseaseSubSubtype" = NA_character_,
"diseaseSubtype" = "melanoma",
"inAchilles" = FALSE,
"inDrive" = TRUE,
"inMarcotte" = FALSE,
"marcotteName" = NA_character_,
"marcotteSubtypeIntrinsic" = NA_character_,
"marcotteSubtypeNeve" = NA_character_,
"marcotteSubtypeThreeReceptor" = NA_character_,
"novartisName" = "a101d",
"novartisPathologistAnnotation" = "Skin:Melanoma",
"novartisPrimarySite" = "skin",
row.names = "A101D_SKIN"
)
)
rowData <- decode(rowData(object)["A1BG_1", c("geneId", "geneName")])
metadata(rowData) <- list()
expect_identical(
object = rowData,
expected = DataFrame(
"geneId" = 1L,
"geneName" = "A1BG",
row.names = "A1BG_1"
)
)
expect_identical(
object = metadata(object)[["dataset"]],
expected = "demeter2_data_v6"
)
expect_true(
isSubset(
x = c(
"AKAP2_11217",
"C10orf113_387638",
"C16orf47_388289",
"C2orf48_348738",
paste(
"LINC01001",
"LOC105377826",
"LOC107984841_100133161",
"105377826",
"107984841",
sep = "_and_"
),
paste(
"LOC100133050",
"LOC102725009_100133050",
"102725009",
sep = "_and_"
)
),
y = metadata(object)[["retiredGenes"]]
)
)
})
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