#' CCLE copy number data
#'
#' @details
#' Gene level copy number data, log2 transformed with a pseudo count of 1.
#' This is generated by mapping genes onto the segment level calls.
#'
#' Inherits from `SummarizedExperiment`.
#' Cells in columns, genes in rows.
#'
#' @export
#' @note Updated 2021-06-09.
#'
#' @return `CCLECopyNumberData`.
setClass(
Class = "CCLECopyNumberData",
contains = "SummarizedExperiment"
)
setValidity(
Class = "CCLECopyNumberData",
method = function(object) {
ok <- validate(
isSubset("log2CopyNumber", assayNames(object)),
isSubset(
x = c(
"chromosome",
"dbXrefs",
"description",
"featureType",
"geneId",
"geneName",
"geneSynonyms",
"mapLocation",
"modificationDate",
"nomenclatureStatus",
"otherDesignations",
"typeOfGene",
"xTaxId"
),
y = colnames(rowData(object))
),
isSubset(
x = c(
"achillesNReplicates",
"age",
"alias",
"cas9Activity",
"ccleName",
"cellLineName",
"cellLineNnmd",
"cultureMedium",
"cultureType",
"depMapId",
"lineage",
"lineageMolecularSubtype",
"lineageSubSubtype",
"lineageSubtype",
"primaryOrMetastasis",
"rrid",
"sampleCollectionSite",
"sangerModelId",
"sex",
"source",
"strippedCellLineName"
## > "cosmicid",
## > "depmapPublicComments",
## > "primaryDisease",
## > "subtype"
## > "wtsiMasterCellId"
),
y = colnames(colData(object))
)
)
if (!isTRUE(ok)) return(ok)
ok <- validateClasses(
object = metadata(object),
expected = list(
## > "missingCells" = "character",
## > "retiredGenes" = "character",
"dataset" = "character",
"date" = "Date",
"packageName" = "character",
"packageVersion" = "numeric_version",
"sessionInfo" = "session_info",
"wd" = "character"
),
subset = TRUE
)
if (!isTRUE(ok)) return(ok)
TRUE
}
)
#' CCLE expression data
#'
#' @details
#'
#' RNA-seq TPM gene expression data for just protein coding genes using RSEM.
#' Log2 transformed, using a pseudo-count of 1.
#'
#' Inherits from `SummarizedExperiment`.
#' Cells in columns, genes in rows.
#'
#' @export
#' @note Updated 2021-06-09.
#'
#' @return `CCLEExpressionData`.
setClass(
Class = "CCLEExpressionData",
contains = "SummarizedExperiment"
)
setValidity(
Class = "CCLEExpressionData",
method = function(object) {
ok <- validate(
isSubset("log2Tpm", assayNames(object)),
isSubset(
x = c(
"chromosome",
"dbXrefs",
"description",
"featureType",
"geneId",
"geneName",
"geneSynonyms",
"mapLocation",
"modificationDate",
"nomenclatureStatus",
"otherDesignations",
"typeOfGene",
"xTaxId"
),
y = colnames(rowData(object))
),
isSubset(
x = c(
"achillesNReplicates",
"age",
"alias",
"cas9Activity",
"ccleName",
"cellLineName",
"cellLineNnmd",
"cultureMedium",
"cultureType",
"depMapId",
"lineage",
"lineageMolecularSubtype",
"lineageSubSubtype",
"lineageSubtype",
"primaryOrMetastasis",
"rrid",
"sampleCollectionSite",
"sangerModelId",
"sex",
"source",
"strippedCellLineName"
## > "cosmicid",
## > "depmapPublicComments",
## > "primaryDisease",
## > "subtype",
## > "wtsiMasterCellId"
),
y = colnames(colData(object))
)
)
if (!isTRUE(ok)) return(ok)
ok <- validateClasses(
object = metadata(object),
expected = list(
## > "missingCells" = "character",
## > "retiredGenes" = "character",
"dataset" = "character",
"date" = "Date",
"packageName" = "character",
"packageVersion" = "numeric_version",
"sessionInfo" = "session_info",
"wd" = "character"
),
subset = TRUE
)
if (!isTRUE(ok)) return(ok)
TRUE
}
)
#' CCLE fusion data
#'
#' @details
#' Inherits from `DataFrame`.
#'
#' @note Updated 2021-02-25.
#' @export
#'
#' @return `CCLEFusionData`.
setClass(
Class = "CCLEFusionData",
contains = "DataFrame"
)
setValidity(
Class = "CCLEFusionData",
method = function(object) {
ok <- validate(
isSubset(
x = c(
"annots",
"ccleCount",
"depMapId",
"ffpm",
"fusionName",
"junctionReadCount",
"largeAnchorSupport",
"leftBreakDinuc",
"leftBreakEntropy",
"leftBreakpoint",
"leftGene",
"rightBreakDinuc",
"rightBreakEntropy",
"rightBreakpoint",
"rightGene",
"spanningFragCount",
"spliceType"
),
y = colnames(object)
)
)
if (!isTRUE(ok)) return(ok)
ok <- validateClasses(
object = metadata(object),
expected = list(
"dataset" = "character",
"filtered" = "logical",
"packageName" = "character",
"packageVersion" = "package_version"
),
subset = TRUE
)
if (!isTRUE(ok)) return(ok)
TRUE
}
)
#' Gene effect co-dependencies
#'
#' @details
#' Inherits from `DataFrame`.
#'
#' @note Updated 2021-07-19.
#' @export
#'
#' @return `Codependencies`.
setClass(
Class = "Codependencies",
contains = "DataFrame"
)
setValidity(
Class = "Codependencies",
method = function(object) {
ok <- validate(
isSubset(
x = c(
"correlation",
"entrezId",
"gene"
),
y = colnames(object)
)
)
if (!isTRUE(ok)) return(ok)
ok <- validateClasses(
object = metadata(object),
expected = list(
"dataset" = "character",
"gene" = "character",
"packageName" = "character",
"packageVersion" = "package_version"
),
subset = TRUE
)
if (!isTRUE(ok)) return(ok)
TRUE
}
)
#' CCLE mutation data
#'
#' @details
#' Inherits from `DataFrame`.
#'
#' @note Updated 2021-02-25.
#' @export
#'
#' @return `CCLEMutationData`.
setClass(
Class = "CCLEMutationData",
contains = "DataFrame"
)
setValidity(
Class = "CCLEMutationData",
method = function(object) {
ok <- validate(
isSubset(
x = c(
"annotationTranscript",
"cDnaChange",
"cgaWesAc",
"chromosome",
"codonChange",
"cosmiChsCnt",
"dbSnpRs",
"dbSnpValStatus",
"depMapId",
"endPosition",
"entrezGeneId",
"exAcAf",
"genomeChange",
"hcAc",
"hugoSymbol",
"isCosmiChotspot",
"isDeleterious",
"isTcgAhotspot",
"ncbiBuild",
"proteinChange",
"rdAc",
"referenceAllele",
"rnAseqAc",
"sangerWesAc",
"startPosition",
"strand",
"tcgAhsCnt",
"tumorSeqAllele1",
"variantAnnotation",
"variantClassification",
"variantType",
"wgsAc"
),
y = colnames(object)
)
)
if (!isTRUE(ok)) return(ok)
ok <- validateClasses(
object = metadata(object),
expected = list(
"dataset" = "character",
"packageName" = "character",
"packageVersion" = "package_version"
),
subset = TRUE
)
if (!isTRUE(ok)) return(ok)
TRUE
}
)
#' Gene effect in cancer cell lines
#'
#' @details
#' Inherits from `SummarizedExperiment`.
#' Cells in columns, genes in rows.
#'
#' @export
#' @note Updated 2021-07-08.
#'
#' @return `GeneEffect`.
#'
#' @seealso
#' - https://depmap.org/portal/achilles/
#' - https://depmap.org/ceres/
#' - https://score.depmap.sanger.ac.uk/
setClass(
Class = "GeneEffect",
contains = "SummarizedExperiment"
)
setValidity(
Class = "GeneEffect",
method = function(object) {
ok <- validate(
hasDimnames(object),
isSubset("effect", assayNames(object))
)
if (!isTRUE(ok)) return(ok)
ok <- validateClasses(
object = metadata(object),
expected = list(
## > "missingCells" = "character",
## > "retiredGenes" = "character",
"dataset" = "character",
"date" = "Date",
"libraryType" = "character",
"packageVersion" = "package_version",
"project" = "character",
"scoringMethod" = "character",
"sessionInfo" = "session_info",
"wd" = "character"
),
subset = TRUE
)
if (!isTRUE(ok)) return(ok)
switch(
EXPR = metadata(object)[["libraryType"]],
"crispr" = {
ok <- validate(
isSubset("probability", assayNames(object)),
isSubset(
x = c(
"achillesNReplicates",
"age",
"alias",
"cas9Activity",
"ccleName",
"cellLineName",
"cellLineNnmd",
"cultureMedium",
"cultureType",
"depMapId",
"lineage",
"lineageMolecularSubtype",
"lineageSubSubtype",
"lineageSubtype",
"primaryOrMetastasis",
"rrid",
"sampleCollectionSite",
"sangerModelId",
"sex",
"source",
"strippedCellLineName"
## Not in "depmap_public_20q2":
## > "wtsiMasterCellId"
## Not in "depmap_public_20q1":
## > "cosmicid",
## > "depmapPublicComments",
## > "primaryDisease",
## > "subtype"
),
y = colnames(colData(object))
)
)
if (!isTRUE(ok)) return(ok)
ok <- validateClasses(
object = metadata(object),
expected = list(
"commonEssentials" = "character",
"controlCommonEssentials" = "character",
"controlNonessentials" = "character"
),
subset = TRUE
)
if (!isTRUE(ok)) return(ok)
},
"rnai" = {
ok <- validate(
isSubset(
x = c(
"ccleId",
"cellLineName",
"disease",
"diseaseSubSubtype",
"diseaseSubtype",
"inAchilles",
"inDrive",
"inMarcotte",
"marcotteName",
"marcotteSubtypeIntrinsic",
"marcotteSubtypeNeve",
"marcotteSubtypeThreeReceptor",
"novartisName",
"novartisPathologistAnnotation",
"novartisPrimarySite"
),
y = colnames(colData(object))
)
)
if (!isTRUE(ok)) return(ok)
}
)
TRUE
}
)
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