#' Import Co-dependency scores
#'
#' @export
#' @note Updated 2021-07-19.
#'
#' @inheritParams params
#'
#' @return `Codependencies`.
#'
#' @seealso
#' - https://forum.depmap.org/t/down-load-of-co-dependencies/175/
#' - Python script for processing of all co-dependency scores:
#' https://gist.github.com/pgm/ac2ac4c664ef81200ce49133cc4cee02
#'
#' @examples
#' x <- Codependencies(gene = "SOX10")
Codependencies <- # nolint
function(
gene,
dataset = c(
"Chronos_Combined",
"CERES_Combined",
"RNAi_merged"
)
) {
assert(isString(gene))
dataset <- match.arg(dataset)
url <- pasteURL(
"depmap.org",
"portal",
"gene",
gene,
paste0(
"top_correlations?",
"dataset_name=", dataset
),
protocol = "https"
)
tmpfile <- .cacheURL(url)
df <- import(file = tmpfile, format = "csv")
df <- as(df, "DataFrame")
colnames(df) <- camelCase(colnames(df), strict = TRUE)
dataset <- df[["dataset"]][[1L]]
df[["dataset"]] <- NULL
metadata(df) <- list(
"dataset" = dataset,
"gene" = gene,
"packageName" = .pkgName,
"packageVersion" = .pkgVersion
)
new(Class = "Codependencies", df)
}
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