CqList-class: S4 class storing the dummy Cq data for performance test.

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

S4 class storing the dummy Cq data for performance test.

Description

A dummy Cq dataset suitable for a package test, typically obtained as the output of make_dummy().

Slots

N

Sample sizes as a numeric vector. The ntrap and npertrap arguments of make_dummy() are inherited to the length of N and each N[i] element, the number of individuals (both for haploidy and diploidy) contained in the ith bulk sample, respectively.

m

Segregation ratio. As for haploidy, m is a matrix with 2 rows and ntrap columns. m[1, i] and m[2, i] stores the number of R (mutant) or S (wild type) individuals while N[i] = sum(m[, i]) specifies the total in the bulk sample. It has 3 rows and ntrap columns as for diploidy. While m[1, i] stands for the number of RR hogozygote individuals, m[2, i] and m[3, i] stand for the numbers of RS heterozygotes and SS homozygotes, respectively.

xR,xS

Numeric vector of the same length with N. xR[i] stores the amount of the template DNA for R allele contained in the ith bulk sample.

housek0,target0,housek1,target1

Numeric vectors of the same lengths with N. Store the generated Cq values.

DCW

ΔCq values measured on the control samples (DNA extract without endonuclease digestion in the RED-ΔΔCq method, or pure R solution in a general ΔΔCq method), DCW, is defined as (target0 - housek0).

DCD

ΔCq values measured on the test samples (samples after endonuclease digestion in the RED-ΔΔCq method, or samples with unknown allele mixing ratios in a general ΔΔCq method), DCD, is defined as (target1 - housek1).

deldel

ΔΔCq value, defined as (DCD - DCW).

RFreqMeasure

A classical index of the allele frequency calculated for each bulk sample, which is defined as (1.0+EPCR)^(-deldel). Note that the values of EPCR and other parameters, such as P or K, are not recorded in the object to avoid leakage of information.

ObsP

As RFreqMeasure can exceed 1 by definition, ObsP is defined as min(RFreqMeasure, 1).

rand.seed

The seed of the random-number generator (RNG) which was fed to the current R session to generate dummy m, xR and xS data.

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