CATS - Revision history

Albrecht: /* Download and installation */

2017-09-04T07:28:10Z

Download and installation

← Older revision		Revision as of 09:28, 4 September 2017
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	</pre>		</pre>
	= Download and installation =		= Download and installation =

			This package only seems to work on linux.


	[http://popgen.dk/software/download/CATS/CATS_1.02.tar.gz Software version 1.02]		[http://popgen.dk/software/download/CATS/CATS_1.02.tar.gz Software version 1.02]

Albrecht: /* heatmap of power */

2015-08-06T16:56:07Z

heatmap of power

← Older revision		Revision as of 18:56, 6 August 2015
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	c<-super.cats(rr,by=length(rr),ncases=765,ncontrols=1274,ncases2=100,ncontrols2=100,		c<-super.cats(rr,by=length(rr),ncases=765,ncontrols=1274,ncases2=100,ncontrols2=100,
	alpha=0.001,prevalence=0.01);		alpha=0.001,prevalence=0.01);
	~~bitmap("PowerFig3.png")~~
	plot(c,main="power",file=NULL)		plot(c,main="power",file=NULL)
	</pre>		</pre>

Albrecht: /* run in R */

2015-08-06T16:50:01Z

run in R

← Older revision		Revision as of 18:50, 6 August 2015
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	<pre>		<pre>
	>library(CATS)		library(CATS)
	>cats(freq=0.2,ncases=500,ncases2=500,ncontrols=1000,ncontrols2=1000,risk=1.5,multiplicative=1)		cats(freq=0.2,ncases=500,ncases2=500,ncontrols=1000,ncontrols2=1000,risk=1.5,multiplicative=1)


	Expected Power is;		Expected Power is;
	For a one-stage study = 0.94		For a one-stage study = 0.94

Albrecht at 16:49, 6 August 2015

2015-08-06T16:49:30Z

← Older revision		Revision as of 18:49, 6 August 2015
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	= Download and installation =		= Download and installation =

	[http://popgen.dk/software/download/CATS/CATS_1.01.tar.gz Software version 1.01]		[http://popgen.dk/software/download/CATS/CATS_1.02.tar.gz Software version 1.02]

	[http://popgen.dk/software/download/CATS/CATS-manual.pdf manual]		[http://popgen.dk/software/download/CATS/CATS-manual.pdf manual]
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	install R package from command line		install R package from command line
	<pre>		<pre>
	wget http://popgen.dk/software/download/CATS/CATS_1.01.tar.gz		wget http://popgen.dk/software/download/CATS/CATS_1.02.tar.gz
	R CMD INSTALL CATS_1.01.tar.gz		R CMD INSTALL CATS_1.02.tar.gz
	</pre>		</pre>

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	<pre>		<pre>
	library(CATS)		library(CATS)
	~~source("superCATS.R")~~
	rr<-seq(1,2,by=0.025)		rr<-seq(1,2,by=0.025)
	c<-super.cats(rr,by=length(rr),ncases=765,ncontrols=1274,ncases2=100,ncontrols2=100,		c<-super.cats(rr,by=length(rr),ncases=765,ncontrols=1274,ncases2=100,ncontrols2=100,
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	<pre>		<pre>
	library(CATS)		library(CATS)
	~~source("superCATS.R")~~
	rr<-seq(1,2,by=0.05)		rr<-seq(1,2,by=0.05)
	maf<-c(0.05,0.1,0.2,0.5)		maf<-c(0.05,0.1,0.2,0.5)

Albrecht at 16:40, 6 August 2015

2015-08-06T16:40:05Z

← Older revision		Revision as of 18:40, 6 August 2015
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	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.		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.

			= cite =

			<pre>
			Skol, AD, Scott, LJ, Abecasis, GR, Boehnke, M (2006). Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat. Genet., 38, 2:209-13.
			</pre>
	= Download and installation =		= Download and installation =

Albrecht: /* Download and installation */

2015-08-06T16:38:19Z

Download and installation

← Older revision		Revision as of 18:38, 6 August 2015
Line 12:		Line 12:
	<pre>		<pre>
	wget http://popgen.dk/software/download/CATS/CATS_1.01.tar.gz		wget http://popgen.dk/software/download/CATS/CATS_1.01.tar.gz
	~~wget~~ R CMD INSTALL CATS_1.01.tar.gz		R CMD INSTALL CATS_1.01.tar.gz
	</pre>		</pre>

Albrecht: /* Download and installation */

2013-08-05T13:56:14Z

Download and installation

← Older revision		Revision as of 15:56, 5 August 2013
Line 9:		Line 9:
	[http://popgen.dk/software/download/CATS/CATS-manual.pdf manual]		[http://popgen.dk/software/download/CATS/CATS-manual.pdf manual]

			install R package from command line
			<pre>
			wget http://popgen.dk/software/download/CATS/CATS_1.01.tar.gz
			wget R CMD INSTALL CATS_1.01.tar.gz
			</pre>

			= run in R =

			<pre>
			>library(CATS)
			>cats(freq=0.2,ncases=500,ncases2=500,ncontrols=1000,ncontrols2=1000,risk=1.5,multiplicative=1)
			Expected Power is;
			For a one-stage study = 0.94
			For first stage in two-stage study = 0.972
			For second stage in replication analysis = 0.784
			For second stage in a joint analysis = 0.929
			pi = 0.5
			</pre>

	= plot examples =		= plot examples =

Albrecht: /* plot examples */

2013-08-05T13:53:11Z

plot examples

← Older revision		Revision as of 15:53, 5 August 2013
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	J2<-c()		J2<-c()
	for(tal in 1:length(RR)){		for(tal in 1:length(RR)){
	temp<-cats(freq=maf[tal2],ncases=1500,ncontrols=1500,ncases2=2000,ncontrols2=2000,risk=RR[tal],pimarkers = 96/300000,alpha=0.05/300000)		temp<-cats(freq=maf[tal2],ncases=1500,ncontrols=1500,ncases2=2000,
			ncontrols2=2000,risk=RR[tal],pimarkers = 96/300000,alpha=0.05/300000)
	J1[tal]<-temp$P.joint		J1[tal]<-temp$P.joint
	temp<-cats(freq=maf[tal2],ncases=1500,ncontrols=1500,ncases2=2000,ncontrols2=2000,risk=RR[tal],pimarkers = 1536/300000,alpha=0.05/300000)		temp<-cats(freq=maf[tal2],ncases=1500,ncontrols=1500,ncases2=2000,
			ncontrols2=2000,risk=RR[tal],pimarkers = 1536/300000,alpha=0.05/300000)
	J2[tal]<-temp$P.joint		J2[tal]<-temp$P.joint
	}		}
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	col=1:length(maf)		col=1:length(maf)

	plot(RR,power.J1536[,1],type=type,lwd=2,ylab="Power",main="Multiplicative model, 1500:1500, 2000:2000",col=col[1],ylim=0:1)		plot(RR,power.J1536[,1],type=type,lwd=2,ylab="Power",main="Multiplicative model,
			1500:1500, 2000:2000",col=col[1],ylim=0:1)
	for(tal2 in 2:length(maf)){		for(tal2 in 2:length(maf)){
	lines(RR,power.J1536[,tal2],lwd=2,col=col[tal2],type=type)		lines(RR,power.J1536[,tal2],lwd=2,col=col[tal2],type=type)
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	source("superCATS.R")		source("superCATS.R")
	rr<-seq(1,2,by=0.025)		rr<-seq(1,2,by=0.025)
	c<-super.cats(rr,by=length(rr),ncases=765,ncontrols=1274,ncases2=100,ncontrols2=100,alpha=0.001,prevalence=0.01);		c<-super.cats(rr,by=length(rr),ncases=765,ncontrols=1274,ncases2=100,ncontrols2=100,
			alpha=0.001,prevalence=0.01);
	bitmap("PowerFig3.png")		bitmap("PowerFig3.png")
	plot(c,main="power",file=NULL)		plot(c,main="power",file=NULL)
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	rr<-seq(1,2,by=0.05)		rr<-seq(1,2,by=0.05)
	maf<-c(0.05,0.1,0.2,0.5)		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);		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)		plot(c2,type="One",main="power2",ylab="Power",xlab="RR",file=NULL,col=1:4)

Albrecht: /* Which design is better */

2013-08-05T13:52:16Z

Which design is better

← Older revision		Revision as of 15:52, 5 August 2013
Line 19:		Line 19:
	rr<-seq(1,2,by=0.05)		rr<-seq(1,2,by=0.05)
	maf<-c(0.05,0.1,0.2,0.5)		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);		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)		plot(c2,type="One",main="power2",ylab="Power",xlab="RR",file=NULL,col=1:4)

Albrecht: /* plot examples */

2013-08-05T13:50:37Z

plot examples

@@ Line 12: / Line 12: @@
 = plot examples =
-==== Simple power plot ====
+==== Which design is better ====
 [[File:catsFig1.png|thumb]]
 <pre>
 library(CATS)
 rr<-seq(1,2,by=0.05)
 maf<-c(0.05,0.1,0.2,0.5)