Genome-wide significance for a GWA scan

Description

Genome-wide significance for a GWA scan. Analysis function is qtscore.

Usage

emp.qtscore(formula , data, snpsubset, idsubset, strata, trait.type="gaussian", 
		times = 200, quiet=FALSE, bcast = 10)

Arguments

All arguments are the same as in and passed intact to the qtscore. See help for this function.

Details

In the analysis of empirical significance, first time the function qtscore is called and result object is saved. Later, the function qtscore is called times times with replace=FALSE in order to generate distribution under the null. Each call, minimal P-value is extracted and compared with original P-values. For a particular SNP, empirical P-value is obtained as a proportion of times minimal Ps from resampled data was less then original P.

The list elements effB, effAB and effBB are the ones obtained from the analysis of the original (not permuted) data set

The function does not yet implement correct analysis for X-linked data.

Value

Object of class scan.gwaa-class

Author(s)

Yurii Aulchenko

See Also

qtscore, emp.ccfast, scan.gwaa-class

Examples

require(GenABEL.data)
data(srdta)
a<-qtscore(qt3~age+sex,data=srdta,snps=c(1:200))
plot(a)
# this does not make sense, as the whole experiment must be analysed, not a small region!
# also, times = 20 is way too small (should be at least 200)
b<-emp.qtscore(qt3~age+sex,data=srdta,snps=c(1:200), times = 20)
plot(b)

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(GenABEL)
Loading required package: MASS
Loading required package: GenABEL.data
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenABEL/emp.qtscore.Rd_%03d_medium.png", width=480, height=480)
> ### Name: emp.qtscore
> ### Title: Genome-wide significance for a GWA scan
> ### Aliases: emp.qtscore
> ### Keywords: htest
> 
> ### ** Examples
> 
> require(GenABEL.data)
> data(srdta)
> a<-qtscore(qt3~age+sex,data=srdta,snps=c(1:200))
Warning messages:
1: In qtscore(qt3 ~ age + sex, data = srdta, snps = c(1:200)) :
  11 observations deleted due to missingness
2: In qtscore(qt3 ~ age + sex, data = srdta, snps = c(1:200)) :
  Lambda estimated < 1, set to 1
> plot(a)
> # this does not make sense, as the whole experiment must be analysed, not a small region!
> # also, times = 20 is way too small (should be at least 200)
> b<-emp.qtscore(qt3~age+sex,data=srdta,snps=c(1:200), times = 20)
   |                                                                               |                                                                      |   0%   |                                                                               |===================================                                   |  50%   |                                                                               |======================================================================| 100%
Warning messages:
1: In qtscore(formula = formula, data = data, snpsubset = snpsubset,  :
  11 observations deleted due to missingness
2: In qtscore(formula = formula, data = data, snpsubset = snpsubset,  :
  Lambda estimated < 1, set to 1
> plot(b)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>