Graphs

Description

Plot graphs to visualize the results of ASP.Bayesian

Usage

 Graphs.Bayesian(M, burn=0, xbins=200, ORlim=c(1,5),
         conf.int=c(0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,0.95), print=TRUE) 

Arguments

Details

Plot two graphs and give associated hexbinplot objects. This two graphs summarize the results of the Bayesian method. The first graph shows the linkage disequilibrium between observed and causal SNPs in abscissae and the OR of causal SNP in ordinates. The second graph displays the alternative allele frequency of causal SNP in abscissae and the alternative allele frequency of observed SNP in ordinates. Before plotting the graphs, the causal odds ratio is transformed. The value of OR is kept if it is superior to 1, otherwise it is inversed. The alternative causal allele frequency is transformes accordingly: if the OR is inferior to 1, the frequency is replaced by its complement to 1. With this transformations, we avoid to obtain two peaks corresponding to equivalent parameter values.

Value

List of 2 hexbin objects:

Author(s)

Claire Dandine-Roulland

References

Dandine-Roulland, Claire and Perdry, Herve. Where is the causal variant? On the advantage of the family design over the case-control design in genetic association studies. Submitted to Eur J Hum Genet

See Also

ASP.Bayesian

Examples

data(ASPData)
B <- ASP.Bayesian(1e5, ASPData$Control, ASPData$Index,
                  ASPData$IBD, 15)
G <- Graphs.Bayesian(B, burn = 5000, xbins=100)

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(ASPBay)
Loading required package: hexbin
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ASPBay/Graphs.Bayesian.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Graphs.Bayesian
> ### Title: Graphs
> ### Aliases: Graphs.Bayesian
> ### Keywords: Graphs
> 
> ### ** Examples
> 
> data(ASPData)
> B <- ASP.Bayesian(1e5, ASPData$Control, ASPData$Index,
+                   ASPData$IBD, 15)
> G <- Graphs.Bayesian(B, burn = 5000, xbins=100)
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
> 
> 
> 
> 
> 
> dev.off()
png 
  2 
>