Common conditional log-likelihood parameterized in terms of delta (
phi / (phi+1))
commonCondLogLikDerDelta(y, delta, der = 0)
list with elements comprising the matrices of count data (or pseudocounts) for the different groups
derivative, either 0 (the function), 1 (first derivative) or 2 (second derivative)
The common conditional log-likelihood is constructed by summing over all of the individual genewise conditional log-likelihoods. The common conditional log-likelihood is taken as a function of the dispersion parameter (
phi), and here parameterized in terms of delta (
phi / (phi+1)). The value of delta that maximizes the common conditional log-likelihood is converted back to the
phi scale, and this value is the estimate of the common dispersion parameter used by all genes.
numeric scalar of function/derivative evaluated at given delta
estimateCommonDisp is the user-level function for estimating the common dispersion parameter.
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