R/calculate_mean_profile.R

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

#' Average the values of same genes in gene expression profile
#'
#' @param file_gene_ave a data.frame
#' @param k a number
#'
#' @return a data.frame, the values of same genes in gene expression profile
#' @export
#'
#' @examples
#' aa <- c("MARCH1","MARC1","MARCH1","MARCH1","MARCH1")
#' bb <- c(2.969058399,4.722410064,8.165514853,8.24243893,8.60815086)
#' cc <- c(3.969058399,5.722410064,7.165514853,6.24243893,7.60815086)
#' file_gene_ave <- data.frame(aa=aa,bb=bb,cc=cc)
#' colnames(file_gene_ave) <- c("Gene", "GSM1629982", "GSM1629983")

#' result <- gene_ave(file_gene_ave, 1)
gene_ave<-function(file_gene_ave, k = 1){
    x <- file_gene_ave[, -k]
    file_gene_ave <- as.matrix(file_gene_ave)
    rownames(file_gene_ave) <- file_gene_ave[,k]
    # x <- file_gene_ave
    ID<- rownames (file_gene_ave)
    ID <- factor(ID,levels=unique(ID))
      
    y <- rowsum(x, ID, reorder=FALSE, na.rm=TRUE)
    n <- rowsum(1L-is.na(x), ID, reorder=FALSE)
    return(y/n)
}