Interval estimation of population allele frequency based on quantitative PCR ΔΔCq measures from bulk samples
Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-ΔΔCq method (Osakabe et al. 2017), as well as general ΔΔCq analysis. Compatible with the Cq measurement of DNA extracted from multiple individuals at once, so called ``group-testing’’, this model assumes that the quantity of DNA extracted from an individual organism follows a gamma distribution. Therefore, the point estimate is robust regarding the uncertainty of the DNA yield.
See the package vignette [Introduction to freqpcr] and published article (Sudo and Osakabe 2021 Molecular Ecology Resources) for the model structure.
Prerequisites are:
Want to know the percentage of the specific allele at the population level (population allele frequency) relative to other allele(s) on the same locus.
For the population in question, multiple DNA solutions (bulk samples) have been obtained, each of which consists of multiple individuals extracted at once.
Quantitative PCR based on the real-time PCR analysis has been performed on each bulk sample and a set of four Cq values is available.
The ΔΔCq value calculated from the Cq quartet represents the allele frequency of the bulk sample (sample allele frequency).
The main function freqpcr() takes as input data the
number of individuals included in each bulk sample (N) and
the set of Cq values (housek0, target0,
housek1, target1) measured for each bulk
sample (since it is a ΔΔCq method, there are usually four Cq
values).
Prior to the estimation with samples with unknown allele ratios,
auxiliary experimental parameters e.g. amplification efficiency during
real-time PCR are required. Functions for estimating experimental
parameters (knownqpcr() and
knownqpcr_unpaired() functions) are also provided, using
multiple DNA solutions with known allele mixing ratios.
Since v0.4.0, the
freqpcr()function has been extended to accept datasets lacking control samples (housek0andtarget0) i.e., a ΔCq method provided the sizes of the auxiliary experimental parameters are known.
library(remotes)
install_github("sudoms/freqpcr")
library(freqpcr)
packageVersion("freqpcr")If there are errors (converted from warning), it might be the case the dependent package ‘cubature’ has been built on a newer version of R (https://github.com/r-lib/remotes/issues/403).
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package 'cubature' was built under R version 3.6.3Then, set the following environment variable:
R_REMOTES_NO_ERRORS_FROM_WARNINGS="true" on you R session
and run install_github() again.
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
install_github("sudoms/freqpcr")library(freqpcr)Dummy Cq data is generated for demo use. As for real qPCR
experiments, you first need to estimate those auxiliary parameters using
samples with known multiple allele-mixing ratios and
knownqpcr() or knownqpcr_unpaired() functions.
See the vignette for detail.
P <- 0.15
K <- 4
# These auxiliary parameters must be pre-defined
EPCR <- 0.97
zeroAmount <- 0.0016
scaleDNA <- 1e-06 # used in make_dummy() but not in freqpcr()
targetScale <- 1.2
baseChange <- 0.2# used in make_dummy() but not in freqpcr()
sdMeasure <- 0.2P: * The population allele frequency to be estimated
K: * The gamma shape parameter of the individual DNA yield
EPCR: * Amplification efficiency per PCR cycle, given as a positive numeric. * When EPCR = 1, template DNA doubles every cycle (EPCR + 1 = 2).
zeroAmount: * (In RED-ΔΔCq method) residual rate of restriction enzyme digestion. * (in general ΔΔCq and ΔCq analyses) small portion of the off-target allele amplified in the PCR process. * It needs to be always specified by the user as a number between 0 and 1, usually near 0.
scaleDNA: * Relative amount of the template DNA (of the housekeeping
gene) compared to the threshold of realtime PCR. * If DNA increases
twofold in a PCR cycle (EPCR = 1), scaleDNA =
10^-6 means Cq value is approximately 20.
targetScale: * Relative DNA amount of the target locus compared with the housekeeping gene.
baseChange: * Relative amount of the template DNA (of the housekeeping gene) before and after the restriction enzyme treatment in the RED-ΔΔCq method (as an involuntary change due to experimental manipulation). * The variable does not exist in other common ΔΔCq and ΔCq methods.
sdMeasure: * The measurement error on each Cq (Ct) value, following Normal(0, sdMeasure)
With four bulk samples, each of which comprises eight haploid individuals
dmy_cq <- make_dummy( rand.seed=71, P=P, K=K, ntrap=4, npertrap=8,
scaleDNA=scaleDNA, targetScale=targetScale,
baseChange=targetScale, EPCR=EPCR,
zeroAmount=zeroAmount,
sdMeasure=sdMeasure, diploid=FALSE )
print(dmy_cq)> print(dmy_cq)
An object of class "CqList"
Slot "N":
[1] 8 8 8 8
Slot "m":
[,1] [,2] [,3] [,4]
[1,] 1 1 1 0
[2,] 7 7 7 8
Slot "xR":
[1] 2.661931e-06 6.163087e-06 3.199384e-06 0.000000e+00
Slot "xS":
[1] 2.216434e-05 3.163697e-05 3.221190e-05 4.018694e-05
Slot "housek0":
[1] 15.52662 14.86406 15.09659 14.84089
Slot "target0":
[1] 15.61207 14.80267 14.53848 14.85648
Slot "housek1":
[1] 17.85924 17.04084 17.54948 17.38438
Slot "target1":
[1] 21.08799 19.55396 20.92745 26.29820
Slot "DCW":
[1] 0.08544953 -0.06139074 -0.55811003 0.01559466
Slot "DCD":
[1] 3.228745 2.513126 3.377968 8.913814
Slot "deldel":
[1] 3.143296 2.574517 3.936078 8.898219
Slot "RFreqMeasure":
[1] 0.11868765 0.17453873 0.06933585 0.00239759
Slot "ObsP":
[1] 0.11868765 0.17453873 0.06933585 0.00239759
Slot "rand.seed":
[1] 71P, K, sdMeasure, and
targetScale are marked unknown.result <- freqpcr( N=dmy_cq@N, housek0=dmy_cq@housek0, target0=dmy_cq@target0,
housek1=dmy_cq@housek1, target1=dmy_cq@target1,
EPCR=EPCR, zeroAmount=zeroAmount, beta=TRUE, print.level=2 )
print(result)> print(result)
An object of class "CqFreq"
Slot "report":
Estimate Fixed (scaled) (scaled.SE) 2.5% 97.5%
P (R-allele frequency) 0.09773189 0 -2.222684 0.60914923 0.03178086 0.2633220
K (gamma shape parameter) 20.92728471 0 3.041054 1.83522515 0.57354355 763.5884712
targetScale (relative amount of target locus) 1.11922896 0 0.112640 0.08911953 0.93985370 1.3328388
Cq measurement error (SD) 0.20973065 0 -1.561931 0.32845070 0.11017528 0.3992451
EPCR (Duplication efficiency of PCR) 0.97000000 1 NA NA NA NA
Slot "obj":
$minimum
[1] 6.094915
$estimate
[1] -2.222684 3.041054 0.112640 -1.561931
$gradient
[1] -3.400973e-05 -8.275889e-05 -5.170087e-05 8.878422e-05
$hessian
[,1] [,2] [,3] [,4]
[1,] 2.71023719 0.05094362 1.168535 -0.1766756
[2,] 0.05094362 0.37630056 2.045198 -0.6539723
[3,] 1.16853469 2.04519835 147.389558 6.4578190
[4,] -0.17667556 -0.65397228 6.457819 11.1504636
$code
[1] 1
$iterations
[1] 12
Slot "cal.time":
user system elapsed
0.72 0.15 0.88result <- freqpcr( N=dmy_cq@N, housek0=dmy_cq@housek0, target0=dmy_cq@target0,
housek1=dmy_cq@housek1, target1=dmy_cq@target1,
K=4,
EPCR=EPCR, zeroAmount=zeroAmount, beta=TRUE, print.level=1 )GitHub repository https://github.com/sudoms/freqpcr
PDF help of the latest version https://github.com/sudoms/freqpcr/releases/latest
Paper https://doi.org/10.1111/1755-0998.13554
Sudo, M.,
& Osakabe, M. (2021). freqpcr: Estimation of population allele
frequency using qPCR ΔΔCq measures from bulk samples. Molecular Ecology
Resources, 00, 1–14. Creative Commons Attribution 4.0 International (CC
BY 4.0)
Author website https://sudori.info/english.html
citation("freqpcr")Masaaki Sudo (https://orcid.org/0000-0001-9834-9857) National Agriculture and Food Research Organization (NARO), Japan
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