dot-knownqpcr_loglike_duo: Log-likelihood of getting Cq values when exact allele mixing...

In freqpcr: Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk Samples

Log-likelihood of getting Cq values when exact allele mixing ratios are known, lacking the quartet structure.

Description

Internal function to return the log-likelihood getting the four Cq measurements under true allele frequency for each bulk sample is known. This is a variant for the 'duo' structure dataset and baseChange is absent. obs.housek0 and obs.target0 are defined for the parity of source code, but they actually accept no data.

Usage

.knownqpcr_loglike_duo(X, A, trueY, Digest, Gene, Cq)

Arguments

X	A numeric vector that stores the current parameter sizes of meanDNA, targetScale, sdMeasure, zeroAmount, and EPCR in log scale.
A	Optionally, you can specify relative DNA content between the samples, as a numeric vector having the same length as the Cq data. If present, A must not include missing values. It is the counterpart of the N argument in freqpcr(), whereas an element of A is not restricted to integer. Because the concentration as a whole is also adjusted with the parameter meanDNA (see Value section), A is used exclusively to reflect the relative contents between the sample solutions. Otherwise, A should be left unspecified (the default is 1 for all replicates).
trueY	A numeric vector having the same length as the Cq data. trueY[i] signifies the exact allele frequency in the ith sample. The values must be between 0 and 1, and NA is not allowed. To improve the estimation accuracy, it is better to include the settings y == 0 (pure S solution) and y == 1 (pure R) in your dataset.

Value

A scalar of the log likelihood.

freqpcr documentation built on March 18, 2022, 7:25 p.m.