assocPvalBySetPlot: Create a Density Plot of P-Values, Highlighting SNPs Within a...

In cpvSNP: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

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 [e-mail]

cpvSNP documentation built on Nov. 8, 2020, 6 p.m.