Description Usage Arguments Details Value Author(s) References Examples
A function to process reference CGH arrays using the fused lasso regression
1 | cghFLasso.ref(CGH.Array, chromosome=NULL, filter=NULL)
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CGH.Array |
numeric vector or matrix. It's the result of one or mutiiple CGH experiments. Each column is the log2 ratios returned from one array experiment and is ordered according to the gene/clones' position on the genome. Missing value should be coded as NA. |
chromosome |
numeric vector. Length should be the same as the row number of |
filter |
numeric vector. Length should be the same as the row number of |
cghFLasso.ref
fits fused lasso regression on reference CGH arrays .
The dynamic programming algorithm developed by N.A.Johnson is used for the model fitting.
numeric matrix representing the smoothed result of the reference arrays.
N. A. Johnson, R. Tibshirani and P. Wang
R. Tibshirani, M. Saunders, S. Rosset, J. Zhu and K. Knight (2004) ‘Sparsity and smoothness via the fused lasso’, J. Royal. Statist. Soc. B. (In press), available at http://www-stat.stanford.edu/~tibs/research.html.
P. Wang, Y. Kim, J. Pollack, B. Narasimhan and R. Tibshirani (2005) ‘A method for calling gains and losses in array CGH data’, Biostatistics 2005, 6: 45-58, available at http://www-stat.stanford.edu/~wp57/CGH-Miner/
R. Tibshirani and P. Wang (2007) ‘Spatial smoothing and hot spot detection using the Fused Lasso’, Biostatistics (In press), available at http://www-stat.stanford.edu/~tibs/research.html.
J. Friedman, T. Hastie. R. Tibshirani (2007) ‘Pathwise coordinate optimization and the fused lasso’.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | library(cghFLasso)
data(CGH)
#############
### Example 1: Process one chromosome vector without using normal references.
CGH.FL.obj1<-cghFLasso(CGH$GBM.y)
plot(CGH.FL.obj1, index=1, type="Lines")
#############
### Example 2: Process a group of CGH arrays and use normal reference arrays.
Normal.FL<-cghFLasso.ref(CGH$NormalArray, chromosome=CGH$chromosome)
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)
### Plot for the first arrays
i<-1
plot(Disease.FL, index=i, type="Single")
title(main=paste("Plot for the ", i ,"th BAC array", sep=""))
### Consensus plot
plot(Disease.FL, index=1:4, type="Consensus")
title(main="Consensus Plot for 4 BAC arrays")
### Plot all arrays
plot(Disease.FL, index=1:4, type="All")
title(main="Plot for all 4 arrays")
### Report and output
report<-summary(Disease.FL, index=1:4)
print(report)
output.cghFLasso(report, file="CGH.FL.output.txt")
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