Piet-package: DNA CNV Analysis Tools Based on Generlized Fused Lasso Model

Description Details Author(s) References Examples

Description

This package provides some segemntation tools for analysis of individual or multiple sequences of CNV data.

Details

Package: Piet
Type: Package
Version: 0.1.0
Date: 2012-02-05
License: GPL (>=2.0)

The most importatn function is GFL that implements the segmentation algorithm for multiple sequences of signals described in Zhang, Lange, and Sabatti (2012). Another function FL is an efficient implementation of fused lasso for segmentation of indiviudal sequences. Fitted segment means resulted from GFL or FL can be used in subsequence CNV analysis.

Author(s)

Zhongyang (Thomas) Zhang

Maintainer: Zhongyang (Thomas) Zhang, zhangzy@ucla.edu

References

  1. Zhongyang Zhang, Kenneth Lange, Roel Ophoff, and Chiara Sabatti. (2010) Reconstructing DNA copy number by penalized estimation and imputation. The Annals of Applied Statistics, 4(4): 1749-1773.

  2. Zhongyang Zhang, Kenneth Lange, and Chiara Sabatti. (2012) Reconstructing DNA copy number by segmentation of multiple sequences. Submitted.

Examples

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## Jointly segment 2 sequences of signals with 100 markers
## Duplications are superimposed on both sequences
Y <- matrix(rnorm(200,0,0.15),100,2)
Y[41:60,] <- rnorm(40,0.3,0.2)
Delta <- matrix(1,100,2)
sigma <- apply(Y,2,FUN="mad")
res <- GFL(Y=Y, Delta, sigma, rho1 = 0.01, rho2 = 0.5*2, rho3 = 0.5*2, 
           obj_c = 1e-4, max_iter = 1000, verbose = FALSE)
plot(res$Beta[,1],type="s")

Piet documentation built on May 2, 2019, 5:19 p.m.