This package provides some segemntation tools for analysis of individual or multiple sequences of CNV data.
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
FL can be used in subsequence CNV analysis.
Zhongyang (Thomas) Zhang
Maintainer: Zhongyang (Thomas) Zhang, firstname.lastname@example.org
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.
Zhongyang Zhang, Kenneth Lange, and Chiara Sabatti. (2012) Reconstructing DNA copy number by segmentation of multiple sequences. Submitted.
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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")
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