Simulation.pickgene(pickgene)
Simulation.pickgene()所属R语言包：pickgene
Yi Lin's simulations for microarray analysis
易林的模拟芯片分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Example simulations
例如模拟
参见----------See Also----------
<CITE>multipickgene</CITE>
<CITE> multipickgene </引用>
举例----------Examples----------
### Note: This uses old pickgene[＃＃注：此使用旧pickgene的]
#detail of the model (7-8). (first run does not include meas error \eta_i)[该模型的细节（7-8）。 （不包括第一次运行测量误差\ eta_i）]
#par(mfrow=c(3,3))[面值（mfrow = C（3,3））]
t<-rnorm(10000,4,2)
changes1<-rep(0,10000)
changes1[1:500]<-rnorm(500)
t1<-t+changes1
changes2<-rep(0,10000)
changes2[1:500]<-rnorm(500)
t2<-t+changes2
s<-rnorm(10000,0,0.1)
cx<-3
cy<-2
t1<-t1+rnorm(10000,0,0.1)
t2<-t2+rnorm(10000,0,0.1)
x<-cx*exp(t1)
y<-cy*exp(t2)
#x<-cx*exp(t1)+rnorm(10000,0,50)[X <-CX * EXP（T1）+ rnorm（10000,0,50）]
#y<-cy*exp(t2)+rnorm(10000,0,40)[Ÿ<-CY * EXP（T2）+ rnorm（10000,0,40）]
xx<-qnorm(rank(x)/(10000+1))
yy<-qnorm(rank(y)/(10000+1))
#hist(x,breaks=100)[历史（X，打破= 100）]
#hist(y,breaks=100)[历史（Y，打破= 100）]
#plot(x,y)[图（X，Y）]
#hist(y[x<=0],breaks=20)[历史（Y [X <= 0]，截断= 20）]
#hist(x[y<=0],breaks=20)[历史（X [Y <= 0]，截断= 20）]
#plot(xx,yy)[图（XX，YY）]
topgenepick<-multipickgene( cbind(xx,yy),condi=0:1,geneID=1:10000, d=1,
npickgene=500)$pick[[1]]$probe
abchangesrank<-rank((-1)*abs(t1-t2))
count <- rep(NA,500)
for( i in 1:500 ) {
topipick <- topgenepick[1:i]
count[i] <- sum( abchangesrank[topipick] <= i )
}
## Figure 2[＃图2]
plot( 1:500, 1:500, type="n",
xlab="Rank of 500 most changed genes by our procedure",
ylab="Number similarly ranked by the 'optimal' procedure",
xaxs="i", yaxs="i" )
lines( 1:500, count, type="s", lty=1, lwd=2 )
abline(0,1)
## Not run: dev.print( hor=F, height=6.5, width=6.5, file="rank1.ps" )[＃无法运行：dev.print（HOR = F高度= 6.5，宽= 6.5，文件=“rank1.ps”）]
#again, but with the additive noise. (includes \eta_i)[再次，但与加性噪声。 （\ eta_i）]
par(mfrow=c(2,2))
t<-rnorm(10000,4,2)
changes1<-rep(0,10000)
changes1[1:500]<-rnorm(500)
t1<-t+changes1
changes2<-rep(0,10000)
changes2[1:500]<-rnorm(500)
t2<-t+changes2
s<-rnorm(10000,0,0.1)
cx<-3
cy<-2
t1<-t1+rnorm(10000,0,0.1)
t2<-t2+rnorm(10000,0,0.1)
### note that noise is very large here (50,40)[＃注意，噪音是非常大的（50,40）]
x<-cx*exp(t1)+rnorm(10000,0,50)
y<-cy*exp(t2)+rnorm(10000,0,40)
xx<-qnorm(rank(x)/(10000+1))
yy<-qnorm(rank(y)/(10000+1))
hist(x,breaks=100)
hist(y,breaks=100)
plot(x,y,cex=0.4)
#hist(y[x<=0],breaks=20)[历史（Y [X <= 0]，截断= 20）]
#hist(x[y<=0],breaks=20)[历史（X [Y <= 0]，截断= 20）]
plot(xx,yy,cex=0.4)
## Not run: dev.print( hor=F, height=6.5, width=6.5, file="simudata.ps" )[＃无法运行：dev.print（HOR = F高度= 6.5，宽= 6.5，文件=“simudata.ps”）]
topgenepick<-multipickgene(cbind(xx,yy),condi=0:1,geneID=1:10000, d=1,
npickgene=500)$pick[[1]]$probe
abchangesrank<-rank((-1)*abs(t1-t2))
count <- rep(NA,500)
for( i in 1:500 ) {
topipick <- topgenepick[1:i]
count[i] <- sum( abchangesrank[topipick] <= i )
}
par(mfrow=c(1,1)) # figure 4[图4]
plot( 1:500, 1:500, type="n",
xlab="Rank of 500 most changed genes by our procedure",
ylab="Number similarly ranked by the 'optimal' procedure",
xaxs="i", yaxs="i" )
lines( 1:500, count, type="s", lty=1, lwd=2 )
abline(0,1)
## Not run: dev.print( hor=F, height=6.5, width=6.5, file="rank2.ps" )[＃无法运行：dev.print（HOR = F高度= 6.5，宽= 6.5，文件=“rank2.ps”）]
### Figure 5[＃＃图5]
genepick <- multipickgene( cbind(xx,yy), condi=0:1, geneID=1:10000, d=1)
## Not run: dev.print( hor=F, height=6.5, width=6.5, file="simutest.ps" )$pick[[1]]$probe[＃不运行：dev.print（贺楼高度= 6.5，宽= 6.5，文件=“simutest.ps”）选择[1] $探针]
npick<-length(genepick$pickedgene)
genepick$pickedgene
npick
count[npick]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-2-26 11:07:06
