R/outputGCT.R

In estimate: Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data

###
### $Id: outputGCT.R 12 2016-09-28 18:25:54Z proebuck $
###


##-----------------------------------------------------------------------------
outputGCT <- function(input.f,
                      output.f) {

    ## Check arguments
    ## input.f - must be character string or connection
    ## output.f - must be character string
   
    if(is.data.frame(input.f)==TRUE) {
        exp.data <- input.f
    } else {
        exp.data <- read.table(input.f, header=TRUE, row.names=1, sep="\t", quote="" )
    }
          
    exp.data1 <- data.frame(NAME=rownames(exp.data),Description=rownames(exp.data),exp.data)
    column1 <- colnames(exp.data1)
    column1[1] <- "NAME"
    column1[2] <- "Description"
    exp.data1$NAME <- factor(exp.data1$NAME)
    exp.data1$Description <- factor(exp.data1$Description)
    levels(exp.data1[,1]) <- c(levels(exp.data1[,1]),"NAME")
    levels(exp.data1[,2]) <- c(levels(exp.data1[,2]),"Description")
    exp.data2 <- rbind(column1,exp.data1)
  
    row1 <- rep("",length(1:ncol(exp.data)))
    row1_2 <- data.frame(row1,row1)
    row1_2 <- t(row1_2)
    No_gene <- nrow(exp.data1)
    No_sample <- (ncol(exp.data1)-2)
    GCT <- matrix(c("#1.2",No_gene,"",No_sample),nrow=2,ncol=2)
    gct <- cbind(GCT,row1_2)
    colnames(gct) <- colnames(exp.data2)
    tmp <- rbind(gct,exp.data2)
    write.table(tmp,output.f, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE)
    invisible(NULL)
}