R/extract_gene_list.R

In neurogenomics/orthogene: Interspecies gene mapping

extract_gene_list <- function(gene_df,
                              gene_input,
                              verbose = TRUE) {
    rown_opts <- gene_input_opts(rownames_opts = TRUE)
    coln_opts <- gene_input_opts(colnames_opts = TRUE)
    col_opts <- gene_input_opts(
        gene_df = gene_df,
        columns_opts = TRUE
    )
    vec_opts <- gene_input_opts(vector_opts = TRUE)

    if (tolower(gene_input) %in% rown_opts) {
        messager("Extracting genes from rownames.", v = verbose)
        genes <- rownames(gene_df)
    } else if (tolower(gene_input) %in% coln_opts) {
        messager("Extracting genes from colnames.", v = verbose)
        genes <- colnames(gene_input)
    } else if (gene_input %in% col_opts) {
        messager("Extracting genes from",
            paste0(gene_input, "."),
            v = verbose
        )
        if (methods::is(gene_df, "data.table")) {
            ### data.table doesn't allow gene_df[,gene_input] syntax
            genes <- gene_df[[gene_input]]
        } else {
            ### Important!:
            # (sparse) matrices don't allow gene_df[[gene_input]] syntax
            genes <- gene_df[, gene_input]
        }
    } else if (gene_input %in% vec_opts){ 
        genes <- unlist(gene_df)
    } else {
        all_opts <- gene_input_opts(
            gene_df = gene_df,
            rownames_opts = TRUE,
            colnames_opts = TRUE,
            columns_opts = TRUE,
            print_friendly = TRUE
        )
        stop_msg <- c(
            "gene_input must match one of:\n",
            all_opts
        )
        stop(stop_msg)
    }
    messager(formatC(length(genes), big.mark = ","),
             "genes extracted.",v=verbose)
    return(genes)
}