plotAndSummarizeAllelicBiasTest: Summarize the allelic bias analysis across SNP regions and...

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

Description

plotAndSummarizeAllelicBiasTest summarizes the allelic bias test across SNP regions and bins by calculating various summary statistics. See the Vignette for more details. TODO

Usage

plotAndSummarizeAllelicBiasTest(SNPhood.o, signThreshold = 0.05,
  fileToPlot = NULL)

Arguments

SNPhood.o	Object of class SNPhood
signThreshold	Numeric(1). Default 0.05. The significance threshold (such as p-value or FDR threshold). Must be between 0 and 1. If the parameter belongs to a plotting function, a horizontal line is drawn at the chosen value. For the allelic bias summary plots, p-values below this threshold and the corresponding allelic fractions are highlighted.
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.

Value

A named list with various elements, each of which summarizes the allelic bias tests with a different focus. TODO

Examples

data(SNPhood, package="SNPhood")
SNPhood.o = testForAllelicBiases (SNPhood.o, readGroups = c("maternal", "paternal"))
SNPhood.o = plotAndSummarizeAllelicBiasTest(SNPhood.o)

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