R/eQTLcatalogue_annotate_tissues.R

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

#' Annotate QTL datasets with metadata
#'
#' Annotate QTL datasets from \emph{eQTL Catalogue} with metadata.
#' @param dat \link[data.table]{data.table} of query results from 
#' \link[catalogueR]{eQTLcatalogue_example_queries}.
#' @param add_tissue_counts Add a new column "Tissue_count" summarizing 
#' the number of datasets per tissue.
#' 
#' @keywords metadata
#' @export
#' @importFrom dplyr mutate select group_by summarise n_distinct rename
#' @importFrom data.table merge.data.table
#' @importFrom stats setNames
#' @examples
#' paths <- catalogueR::eQTLcatalogue_example_queries(
#'     fnames = "BST1__Alasoo_2018.macrophage_IFNg+Salmonella.tsv.gz")
#' dat <- data.table::fread(paths[1], nThread = 1)
#' dat_annot <- catalogueR::eQTLcatalogue_annotate_tissues(dat = dat)
eQTLcatalogue_annotate_tissues <- function(dat,
                                           add_tissue_counts = FALSE) {
    study <- tissue_label <- Tissue_group <- System <- 
        Tissue <- Study <- qtl_id <- unique_id <- NULL;
    meta <- eQTLcatalogue_list_datasets() |>
        dplyr::select(unique_id,
            Study = study,
            Tissue = tissue_label,
            Tissue_group,
            System
        ) |>
        dplyr::mutate(Tissue = gsub("CD16+ monocyte", "monocyte", Tissue)) |>
        dplyr::mutate(Tissue = factor(Tissue,
            levels = unique(Tissue),
            ordered = TRUE
        )) |>
        unique()

    if (!"study" %in% colnames(dat)) {
        dat$Study <- "GWAS"
    }
    if (!"qtl_id" %in% colnames(dat)) {
        dat$qtl_id <- dat$qtl_ID
    }
    dat <- data.table::merge.data.table(dat |> dplyr::rename(Study_id = Study),
        meta,
        by.x = "qtl_id",
        by.y = "unique_id"
    )
    # Add the number of datasets per Tissue as a col
    if (add_tissue_counts) {
        dat_count <- dat |>
            dplyr::group_by(Tissue) |>
            dplyr::summarise(dataset_count = dplyr::n_distinct(qtl_id,
                na.rm = TRUE
            )) |>
            data.table::data.table()
        countDict <- stats::setNames(dat_count$dataset_count, dat_count$Tissue)
        dat$dataset_count <- countDict[dat$Tissue]
        # data.table::merge.data.table(x=dat, y=dat_count, by="Tissue")
        dat$Tissue_count <- paste0(dat$Tissue, " (n=", dat$dataset_count, ")")
        dat$Tissue_count <- factor(dat$Tissue_count,
            levels = unique(dat$Tissue_count),
            ordered = TRUE
        )
    }
    return(dat)
}


#### Deprecation function #####
eQTL_Catalogue.annotate_tissues <- function(...){
  .Deprecated("eQTLcatalogue_annotate_tissues")
  eQTLcatalogue_annotate_tissues(...)
}