R/computeExtrinsicNoise.R

In noise: Estimation of Intrinsic and Extrinsic Noise from Single-Cell Data

computeExtrinsicNoise <- function (reporter1, reporter2) {
    # input: reporter1, reporter2: vectors of normalized reporter gene expression
    
    # compute sample size
    n <- length (reporter1)
    # compute \sum C_i Y_i - n\bar{C}\bar{Y}
    sum.cov <- sum (reporter1*reporter2) - n * mean (reporter1) * mean (reporter2)
    # compute sample correlation
    sample.cor <- cor (reporter1, reporter2)
    
    # unbiased estimator
    unbiased <- sum.cov / (n-1)
    
    # min MSE estimator
    a <- 1/(sample.cor^2) + (n-1)*(1+1/n)
    min.mse <- sum.cov / a
    
    # asymptotic estimator
    asym <- sum.cov / n
    
    # return a list of estimators
    return (list (ELSS=asym, unbiased=unbiased, minMSE=min.mse, asymptotic=asym))
}