In mvaniterson/wbccPredictor: A gene expression or DNA methylation based predictor for white blood cell counts

library(predictcellcomposition)

load/read expression data and covariates

data covariates

convert expression data identifiers to ensembl gene identifiers

data

load predictor

load("RNAseqPredictor.RData")

predicted <- prediction(predictor, data, covariates, ncomp=20)

load/read measured cell percentages

measured

plotting <- function(measured, predicted, xlab="predicted", ylab="measured") {
op <- par(mfcol=c(3, 2), mar=c(4, 4, 3, 1)) for(k in 1:ncol(measured)) { type <- colnames(measured)[k] cme <- cor(predicted[,k], measured[,k]) plot(predicted[,k], measured[,k], main=paste(type, " (correlation: ", round(cme, 2), ")", sep=""), xlab=xlab, ylab=ylab, bty="n", pty="s")
abline(lm(measured[,k]~0+predicted[,k]), col=2, lty=1, lwd=2) abline(0, 1, col="grey", lty=1, lwd=2) grid() } par(op) }

plotting(measured, predicted, xlab="predicted", ylab="measured")

mvaniterson/wbccPredictor documentation built on May 23, 2019, 10:53 a.m.