#' @name show
#' @inherit AcidGenerics::show
#' @note Updated 2021-07-07.
#'
#' @examples
#' data(crispr)
#'
#' ## GeneEffect ====
#' show(crispr)
NULL
## Updated 2021-06-09.
`show,CCLEMutationData` <- # nolint
function(object) {
validObject(object)
showHeader(object)
list <- list(
"mutations" = nrow(object),
"genes" = length(unique(object[["entrezGeneId"]])),
"transcripts" = length(unique(object[["annotationTranscript"]])),
"ncbiBuild" = unique(object[["ncbiBuild"]]),
"variantClassification" = sort(unique(
object[["variantClassification"]]
))
)
showSlotInfo(list)
}
## Updated 2021-07-07.
`show,GeneEffect` <- # nolint
function(object) {
validObject(object)
showHeader(object)
m <- metadata(object)
list <- list(
"dataset" = m[["dataset"]],
"libraryType" = m[["libraryType"]],
"project" = m[["project"]],
"scoringMethod" = m[["scoringMethod"]],
"date" = m[["date"]],
"releaseDate" = m[["releaseDate"]]
)
showSlotInfo(list)
se <- as(object, "SummarizedExperiment")
cat(capture.output(show(se)), sep = "\n")
}
#' @rdname show
#' @export
setMethod(
f = "show",
signature = signature("CCLEMutationData"),
definition = `show,CCLEMutationData`
)
#' @rdname show
#' @export
setMethod(
f = "show",
signature = signature("GeneEffect"),
definition = `show,GeneEffect`
)
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