R/calculate_mean_module.R

In GeoTcgaData: Processing various types of data on GEO and TCGA

#' Find the mean value of the gene in each module
#'
#' @param geneExpress a data.frame
#' @param module a data.frame
#'
#' @return a data.frame, means the mean of gene expression value in
#' the same module
#' @export
#'
#' @examples
#' result <- cal_mean_module(geneExpress,module)
cal_mean_module<-function(geneExpress,module){
    # out <- file.path(tempdir(), "module_result.txt")
    # geneExpress=as.matrix(geneExpress)
    # rownames(geneExpress)<-geneExpress[, 1]
    genes <- rownames(geneExpress)
    output_module <- matrix(0, nrow(module), 2)
    rownames(output_module) <- module[, 1]
    for(i in seq_len(nrow(module))){
        modulen <- unlist(strsplit(module[i, 2], ","))
        modulen <- intersect(modulen, genes)
        modulenDf <- geneExpress[modulen, ]
        output_module[i, ] <- colMeans(modulenDf)   
    }
    as.data.frame(output_module)
}