plot.qq: QQ plot with empirical p-values

In cgmisc-team/cgmisc: Various functions useful in computational genetics, e.g. in GWAS

QQ plot with empirical p-values

Description

Plots qq plot with empirical values and empirical confidence intervals

Usage

plot.qq(data = NULL, obs, emp, N = 30, step = 10, legend = T,
  plot.emp = T, conf.level = 0.95, conf = c(0.025, 0.975), show.pb = T)

Arguments

data	a gwaa.data-class object used to fit the original model
obs	observed values from association test
emp	a matrix of empirical p-values (permutation per row) or a list, result of running polygenic model
N	if polygenic model supplied, a number of permutations to run
step	computation coarseness step
legend	if the legend is to be plotted
plot.emp	plotting empirical values
conf.level	confidence threshold (0.95 by default)
conf	a vector defininy the lower and the upper confidence interval, default 5% CI.
show.pb	a logical indicating whether progress bar will be shown

Author(s)

Marcin Kierczak <[e-mail]>

Examples

## Not run: 
 plot.qq(obs=data.mm[,'Pc1df], conf=c(0.025, 0.975), emp = result[,'Pc1df'], step=10, legend=T, plot.emp=T, conf.level=.95)
 
## End(Not run)

cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.