In michbur/period: System-specific periodicity in qPCR data

Periodicity report

Report generated on r Sys.time() using period_app.

Data with fitted quadratic model

plotFit(res.period())

Linear model coefficient: r signif(res.period()[["COEFS"]][1], 3).

Quadratic model coefficient: r signif(res.period()[["COEFS"]][2], 3).

Residuals of the model with Loess curve

plotRes(res.period())

Local polynomial regression fit standard error: r signif(res.period()[["LOESS"]][["s"]], 3).

Runs test p-value: r signif(res.period()[["RUNS"]][["p.value"]], 3).

Ljung-Box test p-value: r signif(res.period()[["BOX"]][["p.value"]], 3).

Autocorrelation and estimated periodicity

plotAc(res.period())

Estimated periodicity: r paste(round(mean(res.period()[["PERIOD"]], na.rm = TRUE), 1), "\u00B1", round(sd(res.period()[["PERIOD"]], na.rm = TRUE), 1))

Heatmap of position-mapped residuals

plotHm(res.period())

References

A. Spiess, S. Roediger, M. Burdukiewicz, T. Volksdorf and J. Tellinghuisen. “System-specific periodicity in quantitative real-time polymerase chain reaction data questions threshold-based quantitation”. Scientific Reports 6 (2016), p. 38951. DOI: 10.1038/srep38951.

michbur/period documentation built on May 22, 2019, 9:54 p.m.