R/get_gene_info.R

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

#' Get gene info
#' 
#' Get gene info from Biomart
#' 
#' @param genelist Gene list.
#' @inheritParams biomaRt::getBM 
#' 
#' @keywords internal
get_gene_info <- function(genelist,
                          attributes = c("size"),
                          one_row_per_gene = FALSE) {
    requireNamespace("biomaRt")
    requireNamespace("dplyr")
    hgnc_symbol <- NULL;
    genelist <- unique(genelist)
    attributes <- unique(c("hgnc_symbol", "ensembl_gene_id", 
                           attributes, 
                           "start_position", "end_position"))
    message("Retrieving info from biomaRt for ",
            formatC(length(genelist), big.mark = ","),
            " genes.")
    ensembl <- biomaRt::useEnsembl(biomart = "genes", 
                                   dataset = "hsapiens_gene_ensembl")
    # filters = biomaRt::listFilters(ensembl)
    gene_info <- biomaRt::getBM(
        attributes = attributes[!attributes %in% "size"],
        filters = "hgnc_symbol",
        values = genelist,
        mart = ensembl,
        uniqueRows = TRUE
    )
    gene_info$size <- gene_info$end_position - gene_info$start_position
    if (one_row_per_gene) {
        gene_info <- gene_info |>
            dplyr::group_by(hgnc_symbol) |>
            dplyr::slice_head(n = 1) |>
            data.frame()
        rownames(gene_info) <- gene_info$hgnc_symbol
    }
    message("Done.")
    return(gene_info)
}