QQ.plot: QQ plot

In CGEN: An R package for analysis of case-control studies in genetic epidemiology

Description

Create a quantile-quantile plot

Usage

 QQ.plot(pvalues, op=NULL)

Arguments

pvalues	Vector or matrix of p-values. No default.
op	List of options (see details). The default is NULL.

Details

Plots the ranked p-values against their expected order statistics on a minus log base 10 scale. If pvalues is a matrix, then multiple qq plots will be produced, each on a seperate screen. Options list op: Below are the names for the options list op. All names have default values if they are not specified.

• cex Magnification factor for the plotting symbol. The default is 1.

• cex.axis Magnification factor for the axes. The default is 1.

• cex.lab Magnification factor for the axes labels. The default is 1.

• cex.main Magnification factor for the title. The default is 1.

• color The color of the plot and title. The default is "blue".

• figs Two element vector for the number of rows and columns if pvalues is a matrix. The default is NULL.

• min.p All p-values less than min.p will be set to min.p. The default is 1e-16.

• pch The plotting symbol. The default is 21 (circle).

• title Character string or vector for the title of each plot. If pvalues is a matrix, then the column names will be used if title is NULL. The default is NULL.

• xlim The x-axis limits. The default is determined from pvalues.

• ylim The y-axis limits. The default is determined from pvalues.

See Also

Manhattan.plot

Examples

  set.seed(123)
  p <- runif(1000)
  QQ.plot(p)

Example output

Loading required package: survival
Loading required package: mvtnorm
[1] 0

CGEN documentation built on April 28, 2020, 8:08 p.m.