freqpcr_data_tables

Supplementary tables for the "freqpcr" paper.<br>Copyright:Masahiro Osakabe 2017 (Sheet 1)Masaaki Sudo 2021 (Sheet 2--)<br>Sheet 1: The RED-ΔΔCq dataset from Osakabe et al. (2017) Pesticide Biochemistry and Physiology 139 1--8. The quantitative PCR analysis was conducted to quantify the mixing ratios of the R (acaricide resistant) and S (susceptible) alleles of the two-spotted spider mite. As this experiment was the proof-of-concept of the RED-ΔΔCq method, the template DNA solutions were prepared as mixture of R and S at known ratios (the data column "FreqTrue"). PCR conditions and sample pre-treatment are described in Sudo and Osakabe (2021 bioRxiv).<br>Sheet 2Example of the data frame of the Cq values ready for the knownqpcr_unpaired() function of freqpcr package.<br>Sheet 3 and 4Example Cq data frame ready for the knownqpcr() function of the freqpcr package. Sheet 3 is "not recycled" i.e., allowing NAs. Sheet 4 is "recycled" and missing values are filled with the Cq of the (nearly) corresponding experimental conditions. Both are OK for running knownqpcr() function.<br>Please read the supplementary material 2 of the freqpcr paper, as well as the PDF help of the R package, to learn how to use the knownqpcr() or knownqpcr_unpaired() functions.<br>Sheet 5 and 6Summary table for the output data of Experiment 2 (numerical experiment for the confidence interval of the freqpcr package). See Sudo and Osakabe (2021 bioRxiv) for detail.本数据集为“freqpcr”论文的补充表格。 版权所有：2017年 大崎雅弘（Masahiro Osakabe）（工作表1）；2021年 须藤将明（Masaaki Sudo）（工作表2及后续）。 工作表1：源自Osakabe等人2017年发表于《Pesticide Biochemistry and Physiology》（《农药生物化学与生理学》）第139卷第1-8页的RED-ΔΔCq数据集。本实验通过定量PCR（quantitative PCR, qPCR）分析二斑叶螨的抗杀螨剂R等位基因与敏感S等位基因的混合比例。作为RED-ΔΔCq方法的概念验证实验，实验模板DNA溶液按照已知比例混合R与S等位基因（对应数据列"FreqTrue"）。PCR实验条件与样本前处理方法详见须藤将明与大崎雅弘2021年发表于bioRxiv的研究。 工作表2：适配freqpcr软件包中knownqpcr_unpaired()函数的Cq值数据框示例。 工作表3和4：适配freqpcr软件包中knownqpcr()函数的Cq值数据框示例。其中工作表3为“未回收”模式，即允许存在缺失值；工作表4为“回收”模式，缺失值将用（近似）对应实验条件下的Cq值填充。两种模式均可正常运行knownqpcr()函数。 请参阅freqpcr论文的补充材料2，以及该R包（R package）的PDF帮助文档，以了解knownqpcr()或knownqpcr_unpaired()函数的使用方法。 工作表5和6：实验2的输出数据汇总表（针对freqpcr软件包置信区间的数值模拟实验）。详细信息请参阅须藤将明与大崎雅弘2021年发表于bioRxiv的研究。