MultiCNVDetect {MultiCNVDetect} | R Documentation |
Detects copy number variation regions with fused lasso and group lasso regression,solved by BCGD algorithm.
Package: | MultiCNVDetect |
Type: | Package |
Version: | 0.1.0 |
Date: | 2012-10-07 |
License: | GPL(>=2.0) |
The most important function is las_bycgd
that detects CNV regions.
Hao Lin,Qiang Kou.
Maintainer: Hao Lin <sky_linhao@163.com>
sigma<-0.4;a<-0.5;i<-matrix(1:980,980,1);n<-15 J<-matrix(1:n,ncol=1) g<-function(i) 0.25*sigma*sin(a*pi*i) err<-function(i){ set.seed(i); return(rnorm(980,0,sigma)) } y<-matrix(,n,980);set.seed(123) a1<-matrix(rnorm(n,0,1),n,300); a2<-matrix(rnorm(n,0,1),n,380); y[,1:300]<--0.2 y[,301:480]<-0.8 y[,481:980]<--0.2 y15<-y+t(apply(J,1,err))+apply(J,1,g) rm(J,i,a,n,sigma,err,g,a1,a2,y) beta15<-las_bycgd(y15); plot(y15[1,],col=2,xlab="genome order",ylab="log2 ratio", main="n=15(the first sample)",ylim=c(-1.5,2)) lines(beta15[1,],col=4)