R/tic.eval.R

In yufree/xMSanalyzer: xMSanalyzer: R package for data analysis, comparison, and annotation of metabolomics data.

tic.eval <- function(dataA, outloc) {
    
    dir.create(outloc, showWarnings = FALSE)
    setwd(outloc)
    
    tic <- apply(dataA, 2, function(x) {
        x <- replace(x, which(x == 0), NA)
        return(sum(x, na.rm = TRUE))
    })
    
    
    mean_tic <- mean(tic)
    
    cv_tic <- 100 * sd(tic, na.rm = TRUE)/mean(tic, 
        na.rm = TRUE)
    tic_res <- cbind(mean_tic, cv_tic)
    colnames(tic_res) <- c("Average_TIC", "CV_TIC")
    
    
    
    main_lab <- paste("Total TIC using all features\n Average TIC=", 
        mean_tic, "\n%CV TIC=", cv_tic, sep = "")
    
    
    # tiff('barplot_TIC_using_all_features.tiff',width=2000,height=2000,res=300)
    # pdf('TIC_all_features.pdf')
    barplot(tic, cex.names = 0.35, cex.axis = 1, main = main_lab, 
        col = "orange", cex.main = 0.6)
    
    # boxplot(dataA,cex.names=0.35,cex.axis=1,main=main_lab)
    # dev.off()
    
    write.table(tic_res, "TIC_using_all_features.txt", 
        sep = "\t", quote = F, col.name = T, row.names = F)
    names(tic) <- c("sample_TIC")
    write.table(tic, "TIC_each_sample_using_all_features.txt", 
        sep = "\t", quote = F, col.name = T, row.names = T)
    
    # tiff('boxplot_sampleintensity_using_all_features.tiff',width=2000,height=2000,res=300)
    
}