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[http://popgen.dk/software/download/CATS/CATS-manual.pdf manual] | [http://popgen.dk/software/download/CATS/CATS-manual.pdf manual] | ||
= plot examples = | |||
=== Simple power plot ==== | |||
<pre> | |||
library(CATS) | |||
rr<-seq(1,2,by=0.05) | |||
maf<-c(0.05,0.1,0.2,0.5) | |||
c2<-curve.cats(rr,maf,ncases=600,ncontrols=600,ncases2=600,ncontrols2=600,alpha=0.000001,prevalence=0.01); | |||
plot(c2,type="One",main="power2",ylab="Power",xlab="RR",file=NULL,col=1:4) | |||
lines.cats(c2,type="Replication",lty=3) | |||
lines.cats(c2,type="Joint",lty=2) | |||
lines.cats(c2,type="First",lty=4) | |||
legend("left",c("One stage","Joint","Relication","First Stage"),lty=1:4,bty="n") | |||
</pre> | |||
Revision as of 14:24, 5 August 2013
joint power of a non-symetric two stage GWA design
R package for power estimation for a two-stage genome-wide association design. This is a modification of the code from Skol et al 2006, nat genet. so that the relative risk, case-control ratios and allele frequencies are allowed to vary between stages.
Download and installation
plot examples
Simple power plot =
library(CATS)
rr<-seq(1,2,by=0.05)
maf<-c(0.05,0.1,0.2,0.5)
c2<-curve.cats(rr,maf,ncases=600,ncontrols=600,ncases2=600,ncontrols2=600,alpha=0.000001,prevalence=0.01);
plot(c2,type="One",main="power2",ylab="Power",xlab="RR",file=NULL,col=1:4)
lines.cats(c2,type="Replication",lty=3)
lines.cats(c2,type="Joint",lty=2)
lines.cats(c2,type="First",lty=4)
legend("left",c("One stage","Joint","Relication","First Stage"),lty=1:4,bty="n")