Last data update: 2014.03.03

R: Functions for inspecting population substructure
qqpvalR Documentation

Functions for inspecting population substructure

Description

This function plots ranked observed p values against the corresponding expected p values in -log scale.

Usage

qqpval(p, pch=16, col=4, ...)

Arguments

p

a vector of p values

pch

symbol to use for points

col

color for points

...

other plot arguments

Value

A plot

See Also

GenomicControl, WGassociation

Examples

data(SNPs)
datSNP<-setupSNP(SNPs,6:40,sep="")
res<-WGassociation(casco,datSNP,model=c("do","re","log-add"))

# observed vs expected p values for recessive model
qqpval(recessive(res))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SNPassoc)
Loading required package: haplo.stats
Loading required package: survival
Loading required package: mvtnorm
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/SNPassoc/qqpval.Rd_%03d_medium.png", width=480, height=480)
> ### Name: qqpval
> ### Title: Functions for inspecting population substructure
> ### Aliases: qqpval
> ### Keywords: utilities
> 
> ### ** Examples
> 
> data(SNPs)
> datSNP<-setupSNP(SNPs,6:40,sep="")
> res<-WGassociation(casco,datSNP,model=c("do","re","log-add"))
> 
> # observed vs expected p values for recessive model
> qqpval(recessive(res))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>