plotAndSummarizeAllelicBiasTest {SNPhood} | R Documentation

## Summarize the allelic bias analysis across SNP regions and bins and visualize some of the results.

### 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)

[Package SNPhood version 1.12.0 Index]