Description Details Note Author(s) References See Also Examples
Performs a modification of the fused LASSO for SNP subset selection in genetic association studies. The LD LASSO requires densely spaced SNP data and haplotype block structure.
The ldlasso package is a collection of functions designed to apply the LD LASSO methodology as described in Younkin and Rao 2010. Functions usesful for displaying the results are also included.
Package: | ldlasso |
Version: | 2.0 |
Date: | February 1, 2011 |
See the vignette 'ldlasso_vignette.pdf' in ldlasso package directory
doc/.
For a package useful for creating haplotype block boundaries see
MATILDE by Pattaro et al., available at http://astor.som.jhmi.edu/~gp/software/matilde/
The following function may be used to create block boudaries with MATILDE.
find.bounds <- function( block.obj, prob.threshold = 0.95, B = 1e4, frac = 2 ){
Xa <- as.double.snp.data(block.obj@gtdata)
X1 <- ifelse( Xa == 0, "A", "B" )
X2 <- ifelse( Xa == 2, "B", "A" )
X <- makeGenotypes(matrix(paste(X1,X2,sep="/"), byrow = F, ncol = dim(Xa)[2] ))
LD.obj <- LD(X)
null.X <- null.density(X)
nXr <- data.frame(null.X$x, null.X$yR)
names(nXr) <- c("x", "y")
matilde.obj <- matilde(LD.obj$r^2, nXr, B=B)
n <- length(matilde.obj$L)
b.vec <- apply(matilde.obj$b[(n/frac):n,], 2, mean)
block.cood <- as.numeric((b.vec >= prob.threshold))
return( list( matilde.obj = matilde.obj, prob.threshold = prob.threshold, block.cood = block.cood ) )
}
Samuel G. Younkin
<samuel.younkin@gmail.com>
Samuel Younkin, Joseph Nadeau, Robert Elston and J. Sunil Rao, "The Linkage Disequilibrium LASSO for SNP Selection in a Genetic Association Study of Late Onset Alzheimer Disease," Technical Report, 2010
ld_lasso_method, ld_lasso, plot_ldlasso, plot_beta, heatmap
1 2 3 4 5 6 7 | # Load example data
data(ldlasso_example)
ls()
plot_ldlasso( ldlasso.obj )
heatmap(ldlasso.obj)
|
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