R/get-expression.R

In churchill-lab/qtl2api: QTL2 API Library

#' Get the expression data.
#'
#' @param dataset The dataset object.
#' @param id The unique id in the dataset.
#'
#' @return a named `list` with 2 elements.
#' \itemize{
#'   \item data - a `tibble` with samples and data
#'   \item datatypes - a `list` of all the types and the unique values
#' }
#'
#' @export
get_expression <- function(dataset, id) {
    # make sure annotations, data, and samples are synchronized
    ds <- synchronize_dataset(dataset)

    # check if id exists
    if (!any(id == colnames(ds$data))) {
        stop(sprintf("Cannot find id '%s' in dataset", id))
    }

    if (invalid(ds$covar_info)) {
        datatypes <- NULL
    } else {
        datatypes <- list()
        for (i in ds$covar_info$sample_column) {
            stopifnot(!is.null(ds$annot_samples[[i]]))

            if (is.factor(ds$annot_samples[[i]])) {
                # preserve order
                datatypes[[i]] <-
                    levels(ds$annot_samples[[i]])
            } else {
                datatypes[[i]] <-
                    gtools::mixedsort(unique(ds$annot_samples[[i]]))
            }
        }
    }

    # only pass back the columns we need
    samples <- ds$annot_samples %>%
        dplyr::select(
            sample_id = ds$sample_id_field,
            dplyr::all_of(names(datatypes))
        )

    # bind the data
    expression_temp <- tibble::tibble(
        sample_id  = rownames(ds$data),
        expression = ds$data[, id]
    )

    output <- samples %>%
        dplyr::inner_join(
            expression_temp,
            by = "sample_id"
        )

    list(
        data      = output,
        datatypes = datatypes
    )
}