plotFDRResults: Graphically summarize the results of the allelic bias...

In SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

Description

plotAllelicBiasResults graphically summarizes the results of the allelic bias analysis for a specific dataset and region.

Usage

plotFDRResults(SNPhood.o, dataset, FDRThreshold = NULL, fileToPlot = NULL,
  printPlot = TRUE, returnOnlyPlotNotObject = FALSE, verbose = FALSE)

Arguments

SNPhood.o	Object of class SNPhood
dataset	Numeric(1) or Character(1). Single dataset that should be used for plotting, either specified as integer (such as 1, value must be between 1 and the total number of datasets as defined in the object) or its annotation (name must appear in the dataset names as obtained via the function annotationDatasets).
FDRThreshold	Numeric(1) or NULL. Default NULL. If set to a value between 0 and 1, a horizontal line will be drawn in the FDR summary plot to indicate at which p-value threshold the FDR reaches the user-defined value. Additionally, the maximum p-value threshold from the FDR summary data will be printed for which thr FDR is below the specified threshold.
fileToPlot	Character(1) or NULL. Default NULL. Filename of the PDF file for the output plots. If set to NULL, plots will be plotted to the currently active device.
printPlot	Logical(1). Default TRUE. Should the plots be printed? Only relevant if fileToPlot is set to NULL; otherwise, the plots are always printed to the output file.
returnOnlyPlotNotObject	Logical(1). Default FALSE. If set to TRUE, only the plots are returned but not the actual object. Otherwise, for consistancy among the various visualization functions, the SNPhood object is always returned, while the plots are either written to a PDF file as specified by the parameter fileToPlot and/or to the currently active graphics device (i.e., the console usually)
verbose	Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

the generated ggplot2 plot(s) as list for further processing. May contain multiple plots, depending on the function. The plot(s) can then be plotted individually or modified arbitrarily as the user wants. For example, if multiple plots are returned and the plots have been saved in a variable called plots.l, simply type plots.l[[1]] to view the first plot.

Examples

data(SNPhood.o, package="SNPhood")
SNPhood.o = testForAllelicBiases(SNPhood.o, readGroups = c("maternal", "paternal"))
# Plot FDR results for first dataset
plotFDRResults(SNPhood.o, annotationDatasets(SNPhood.o)[1], FDRThreshold = NULL, fileToPlot = NULL)

# Plot FDR results for second dataset, save in file and also detemrine p-value treshold for which the FDR is below 10%
plotFDRResults(SNPhood.o, annotationDatasets(SNPhood.o)[1], FDRThreshold = 0.1, fileToPlot = "FDR_summary.pdf")

SNPhood documentation built on Nov. 8, 2020, 6:22 p.m.