R/rep.R

In huerqiang/GeoTcgaData: Processing Various Types of Data on GEO and TCGA

#' Handle the case where one id corresponds to multiple genes
#'
#' @param input_file input file, a data.frame or a matrix, 
#' the first column should be genes.
#' @param string a string, sep of the gene
#'
#' @return a data.frame, when an id corresponds to multiple genes,
#' the expression value is assigned to each gene
#' @export
#'
#' @examples
#' aa <- c("MARCH1 /// MMA", "MARC1", "MARCH2 /// MARCH3", 
#'     "MARCH3 /// MARCH4", "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")
#' input_file <- data.frame(aa = aa, bb = bb, cc = cc)
#'
#' repAssign_result <- repAssign(input_file, " /// ")
#'
repAssign <- function(input_file, string) {
    name <- colnames(input_file)[1]
    genelist <- strsplit(input_file[, 1], string)
    geneLength <- unlist(lapply(genelist, length))
    input_file <- input_file[, -1]
    output <- apply(input_file, 2, rep, times = geneLength)
    output2 <- matrix(as.numeric(output), nrow = nrow(output))
    colnames(output2) <- colnames(output)
    output2 <- data.frame(unlist(genelist), output2, check.names = FALSE)
    colnames(output2)[1] <- name
    output2
}

#' Handle the case where one id corresponds to multiple genes
#'
#' @param input_file input file, a data.frame or a matrix, 
#' the first column should be genes.
#' @param string a string,sep of the gene
#'
#' @return a data.frame, when an id corresponds to multiple genes,
#' the expression value is deleted
#' @export
#'
#' @examples
#' aa <- c("MARCH1 /// MMA", "MARC1", "MARCH2 /// MARCH3", 
#'     "MARCH3 /// MARCH4", "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")
#' input_file <- data.frame(aa = aa, bb = bb, cc = cc)
#' repRemove_result <- repRemove(input_file, " /// ")
repRemove <- function(input_file, string) {
    unKeep <- grep(string, input_file[, 1])
    if (length(unKeep) > 0) input_file <- input_file[-unKeep, ]
    input_file
}