Package: freqpcr 0.4.0
freqpcr: Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk Samples
Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017, <doi:10.1016/j.pestbp.2017.04.003>), as well as general DeltaDeltaCq 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.
Authors:
freqpcr_0.4.0.tar.gz
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freqpcr.pdf |freqpcr.html✨
freqpcr/json (API)
NEWS
| # Install 'freqpcr' in R: |
| install.packages('freqpcr', repos = c('https://sudoms.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sudoms/freqpcr/issues
bioinformaticsfrequency-estimationpcrstatistics
Last updated 3 years agofrom:10021cb1f3. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 30 2025 |
| R-4.5-win | OK | Mar 30 2025 |
| R-4.5-mac | OK | Mar 30 2025 |
| R-4.5-linux | OK | Mar 30 2025 |
| R-4.4-win | OK | Mar 30 2025 |
| R-4.4-mac | OK | Mar 30 2025 |
| R-4.4-linux | OK | Mar 30 2025 |
| R-4.3-win | OK | Mar 30 2025 |
| R-4.3-mac | OK | Mar 30 2025 |
Exports:freqpcrknownqpcrknownqpcr_unpairedmake_dummysim_dummy
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Log-likelihood of obtaining Cq values under given parameter set. | .freqpcr_loglike |
| Log-likelihood when sample allele ratio is continuous. | .freqpcr_loglike_cont |
| Output object of 'freqpcr()'. | CqFreq CqFreq-class |
| S4 class storing the dummy Cq data for performance test. | CqList CqList-class |
| Estimate population allele frequency from the set of Cq measurements. | freqpcr |
| Estimate auxiliary parameters using samples with known allele ratios. | knownqpcr |
| Estimate auxiliary parameters when the sample pairs are incomplete. | knownqpcr_unpaired |
| Generate dummy DNA dataset ready for allele-frequency estimation. | make_dummy |
| Simulate freqpcr estimation based on user-generated dummy data. | sim_dummy |
