R/internal-import.R

In acidgenomics/r-depmapanalysis: DepMap Analysis Utilities

#' Cache URL into package
#'
#' @note Updated 2021-07-08.
#' @noRd
.cacheURL <- function(url, ...) {
    alert(sprintf("Downloading DepMap file {.url %s}.", url))
    cacheURL(url, pkg = .pkgName, ...)
}



#' Import cell line sample metadata
#'
#' @note Updated 2021-07-19.
#' @noRd
.importCellLineSampleData <-  # nolint
    function(dataset) {
        url <- datasets[[dataset]][["metadata"]][["sample_info"]][["url"]]
        df <- .importDataFile(
            url = url,
            rownamesCol = 1L,
            return = "DataFrame"
        )
        assert(is(df, "DataFrame"))
        colnames(df) <- camelCase(colnames(df))
        if (
            !isSubset("cellLineName", colnames(df)) &&
            isSubset("strippedCellLineName", colnames(df))
        ) {
            ## e.g. "depmap_public_20q3".
            df[["cellLineName"]] <- df[["strippedCellLineName"]]
        } else if (
            !isSubset("cellLineName", colnames(df)) &&
            isSubset("ccleId", colnames(df))
        ) {
            x <- df[["ccleId"]]
            x <- vapply(
                X = strsplit(x = x, split = "_", fixed = TRUE),
                FUN = `[`,
                i = 1L,
                FUN.VALUE = character(1L)
            )
            df[["cellLineName"]] <- x
        }
        assert(isSubset("cellLineName", colnames(df)))
        df
    }



#' Import a DepMap data file
#'
#' @note Updated 2021-07-07.
#' @noRd
.importDataFile <- function(
    url,
    format = c("csv", "tsv"),
    rownamesCol = NULL,
    engine = "data.table",
    return = c("DataFrame", "matrix")
) {
    assert(
        isAURL(url),
        isScalar(rownamesCol) || is.null(rownamesCol),
        isString(engine)
    )
    format <- match.arg(format)
    return <- match.arg(return)
    tmpfile <- .cacheURL(url = url)
    df <- import(file = tmpfile, format = format, engine = engine)
    if (isScalar(rownamesCol)) {
        if (!isString(rownamesCol)) {
            rownamesCol <- colnames(df)[[rownamesCol]]
        }
        assert(isSubset(rownamesCol, colnames(df)))
        rownames(df) <- df[[rownamesCol]]
    }
    out <- switch(
        EXPR = return,
        "DataFrame" = as(df, "DataFrame"),
        "matrix" = {
            if (hasRownames(df)) df[[rownamesCol]] <- NULL
            as.matrix(df)
        }
    )
    out <- makeDimnames(out)
    out
}



#' Import a DepMap file containing gene identifiers
#'
#' @note Updated 2021-07-08.
#' @noRd
.importGeneDataFile <-
    function(url) {
        df <- .importDataFile(
            url = url,
            ## Don't use 'data.table' here.
            engine = "base",
            return = "DataFrame"
        )
        colnames(df) <- camelCase(colnames(df))
        if (identical(colnames(df), c("geneSymbol", "geneId"))) {
            ## e.g. DEMETER2 control files.
            vec <- paste0(df[["geneSymbol"]], " (", df[["geneId"]], ")")
        } else {
            ## e.g. DepMap current public release files.
            assert(
                identical(colnames(df), "gene"),
                isCharacter(df[["gene"]])
            )
            vec <- df[["gene"]]
        }
        vec <- sort(vec)
        vec
    }