R/mark.genes.R

In SingerLab/gac: Genetic Analysis of Cells

#' Mark genes
#'
#' Produces a named list with gene name and bin.id to use in ComplexHeatmap::anno_mark
#'
#' @param cnr  the cnr bundle
#'
#' @param gene.list the list of genes you wish to mark
#'
#' @param identifier name of the column with gene identifiers
#'
#'
#' @return
#' returns a vector of named gene.list (gg) w/their rownames/bin.id
#' 
#' @examples
#' 
#' data(cnr)
#'
#' aa <- mark.genes(cnr, gene.list = c("CDK4", "MDM2"))
#'
#' \dontrun{
#' geneAnno <- ComplexHeatmap::rowAnnotation(genes = anno_mark(at = aa, labels = names(aa)))
#' }
#' 
#' @export
mark.genes <- function(cnr, gene.list, identifier = "hgnc.symbol") {
    ## genes to mark in Heatmap

    ggL <- cnr$gene.index[, identifier] %in% gene.list

    na <- setdiff(gene.list, cnr$gene.index[,identifier])

    if(length(na) > 0) {
        warning(na)
    }
    
    gg <- cnr$gene.index[ggL, "bin.id"]
    names(gg) <- cnr$gene.index[ggL, "hgnc.symbol"]
    return(gg)
    
} ## mark.genes