WarneckeCalibrationPlot: Warnecke calibration plots

In lb664/MethylCal: MethylCal: Bayesian Calibration of Methylation Levels

Description

Visualisation of Warnecke calibration of the standard control experiment.

Usage

WarneckeCalibrationPlot(data, Target = NULL, level = 0.95,
  dir = NULL, cex_par = 1.25)

Arguments

data	Formatted input data frame obtained from the function Formatting.
Target	Name of the target DMR/CpG island/gene to be visualised.
level	Level of significance of prediction interval obtained with Warnecke's calibration curve.
dir	In Unix-specific OS, user-specified directory where the plots in pdf format are saved. If the directory is not specified, figures are saved in the current working directory.
cex_par	Number indicating the amount by which plotting text and symbols should be scaled relative to the default (cex_par = 1).

Value

This function returns four plots. The first scatterplot depicts the values of the recorded apparent methylation levels at each Actual Methylation Percentage (AMP) with superimposed Warnecke's calibration curve (Warnecke et al., 1997) for each CpG (red dashed line). The second plot presents the apparent methylation levels at consecutive CpGs stratified by AMPs with superimposed the (1-level)% prediction interval (dashed-dotted red lines). The third plot is the scatterplot of the corrected methylation levels at each AMP for all CpGs within a DRM/CpG island/gene. Finally, the fourth plot is the hyperbolic coefficient (Moskalev et al., 2011) of the corrected methylation levels regressed on the AMPs for each CpG.

In Unix-specific OS, figures are saved in the current directory, unless otherwise specified by the user, in pdf format. In Windows OS, figures are printed on the screen.

References

Ochoa E, Zuber V, Fernandez-Jimenez N, Bilbao JR, Clark GR, Maher ER and Bottolo L. MethylCal: Bayesian calibration of methylation levels. Submitted. 2019.

Moskalev EA, Zavgorodnij MG, Majorova SP, Vorobjev IA, Jandaghi P, Bure IV, Hoheisel JD. Correction of PCR-bias in quantitative DNA methylation studies by means of cubic polynomial regression. Nucleic Acids Res. 2011; 39(11):e77. (PubMed)

Warnecke PM, Stirzaker C, Melki JR, Millar DS, Paul CL, Clark SJ. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res. 1997; 25(21):4422-6. (PMC)

Examples

data(BWS_data)
AMP = c(0, 25, 50, 75, 100)
data = Formatting(BWS_data, AMP = AMP)
WarneckeCalibrationPlot(data, Target = "KCNQ1OT1")

data(Celiac_data)
AMP = c(0, 12.5, 25, 37.5, 50, 62.5, 87.5, 100)
data = Formatting(Celiac_data, AMP = AMP)
WarneckeCalibrationPlot(data, Target = "NFKBIA", level = 0.99)

lb664/MethylCal documentation built on May 23, 2019, 4:02 a.m.