#' Import CCLE fusion data
#'
#' @export
#' @note Updated 2021-07-09.
#'
#' @inheritParams params
#' @param filtered `logical(1)`.
#' Load filtered fusion calls.
#'
#' @return `CCLEFusionData`.
#'
#' @examples
#' object <- CCLEFusionData()
#' dim(object)
CCLEFusionData <- # nolint
function(dataset, filtered = TRUE) {
dataset <- match.arg(dataset)
assert(isFlag(filtered))
key <- ifelse(
test = filtered,
yes = "fusions",
no = "fusions_unfiltered"
)
url <- datasets[[dataset]][["ccle"]][[key]][["url"]]
assert(isAURL(url))
df <- .importDataFile(url = url, format = "csv", rownamesCol = NULL)
assert(is(df, "DataFrame"))
colnames(df) <- camelCase(colnames(df), strict = TRUE)
## e.g. "depmap_public_20q3".
colnames(df)[colnames(df) == "xFusionName"] <- "fusionName"
df <- encode(df)
metadata(df) <- list(
"dataset" = dataset,
"filtered" = filtered,
"packageName" = .pkgName,
"packageVersion" = .pkgVersion
)
new("CCLEFusionData", df)
}
formals(CCLEFusionData)[["dataset"]] <- .formalsList[["depmapDataset"]]
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