assocPvalBySetPlot {cpvSNP} | R Documentation

## Create a Density Plot of P-Values, Highlighting SNPs Within a Gene Set

### Description

Plots association test p-values, highlighting p-values within gene sets.

### Usage

    assocPvalBySetPlot(pvals, set, title = "", geneSetColor = "red",
       xlab = expression(-log[10]~p-value),
       ylab = "Density",
       xlim = NULL, ylim = NULL,
      ...)

### Arguments

`pvals` | A numerical vector of p-values with names corresponding to elements listed in the geneIds slot in the set object.
`set` | An object of class `GeneSet` where geneIds holds the items of each set corresponding to the pvals.
`title` | A character string containing the title of the plot. Default is "", a blank title.
`geneSetColor` | A character vector holding the color the highlighted SNPs in the set object should be. Default is `red`.
`xlab` | A character vector with the label for the x-axis on the plot. Default is `-log10(PValue)`.
`ylab` | A character vector holding the label for the y-axis on the plot. Default is `Density`.
`xlim` | A vector of two numeric values with the limits of plotting on the x-axis. By default, the range of the x-axis values will be determined from the data.
`ylim` | A vector with two numeric values used as limits for plotting on the y-axis. By default, the range of the y-axis values will be determined from the data.
`...` | Further arguments to be passed to the plotting methods, such as graphical parameters.

### Details

Creates a density plot of all -log10(p-value), and overlaying a density plot of -log10(p-value) for SNPs within a gene set of interest.

### Value

Creates a plot.

### Author(s)

Jason Hackney, Jessica Larson, Caitlin McHugh mchughc@uw.edu

[Package cpvSNP version 1.20.0 Index]