freqpcr

Posted on 18.01.2021 - 10:08 by Masaaki Sudo

The R package 'freqpcr' (Sudo and Osakabe in prep.) (https://github.com/sudoms/freqpcr) provides a procedure for interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017) as well as general DeltaDeltaCq analysis. Compatible with the Cq measurement on DNA extract from multiple individuals at once, so called ``group-testing.'' The model assumes the quantity of DNA extracted from an individual organism to follow a gamma distribution, thereby the point estimate is robust to the uncertainty of DNA yield.

The collection on figshare.com includes the estimation results of freqpcr() in the numerical experiment in order to assess the estimation accuracy. The experimental procedure will be published as the supplementary materials of the article (Sudo and Osakabe in prep.) (publication information is added here).

CITE THIS COLLECTION

Select your citation style and then place your mouse over the citation text to select it.
Sudo, Masaaki (2021): freqpcr. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.5258027.v1
or

FUNDING

The work was supported by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics-based Technology for Agricultural Improvement): PRM05 to MO and PRM07 to MS.

SHARE

email
need help?