R/compare_intensities_cortest.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

compare_intensities_cortest <- function(other_feats, y, merge.eval.pvalue) {
    cortest_sum = apply(other_feats, 1, function(x) {
        
        x <- as.matrix(x)
        y <- as.matrix(y)
        yind <- which(y == 0)
        xind <- which(x == 0)
        naind <- c(yind, xind)
        
        if (dim(x)[1] > dim(y)[1]) {
            x <- t(x)
        }
        
        if (dim(y)[1] > dim(x)[1]) {
            y <- t(y)
        }
        if (length(naind) > 0) {
            x <- x[-naind]
            y <- y[-naind]
            
        }
        # if(max(x)!=0 & max(y)!=0)
        
        
        if (length(x) > 2 & length(y) > 2) {
            cortest_res = try(cor.test(as.numeric(x), as.numeric(y), 
                method = "pearson"), silent = TRUE)
            if (is(cortest_res, "try-error")) {
                cortest_pval <- 1
                cortest_est <- 0
            } else {
                cortest_pval = cortest_res$p.value
                cortest_est = cortest_res$estimate
                if (cortest_est < 0.1) {
                  cortest_pval = 1
                }
            }
        } else {
            cortest_pval <- 1
        }
        
        return(cortest_pval)
    })
    return(cortest_sum)
}