Nothing
test.correlation<-function (x, param, method.cor = "kendall", method.padj = "BH", file = "correlation_plot.pdf")
{
data <- select.measurements(x)
pvals <- c(NULL)
tauvals <- c(NULL)
for (k in 1:ncol(data[[1]])) {
rval <- cor.test(data[[1]][, k], data[[4]][, param], method = method.cor)
pvals <- c(pvals, rval[[3]][1])
tauvals <- c(tauvals, rval[[4]][1])
}
adjustedp <- p.adjust(pvals, method = method.padj)
count <- 0
pdf(file = file)
for (k in 1:ncol(data[[1]])) {
count <- count + 1
par(lwd = 2)
plot(data[[1]][, k], data[[4]][, param], xlab = paste(data[[3]]["target", k], "expression"), ylab = param,
main = c(paste("correlation of", data[[3]]["target", k], "expression"), paste("to", param),
paste("correlation: ", round(tauvals[count], digits = 3), " ", "p-value: ",
signif(adjustedp[count], digits = 4))), pch = 2, col = "red")
elem<-lm(data[[4]][, param] ~ data[[1]][, k])
if(!any(is.na(elem$coefficients))){
abline(elem, col = "darkgreen")
}
}
dev.off()
}
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