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ldlasso (version 3.2)

ld_lasso_method: The LD LASSO function

Description

This function implements a method for the automatic selection of parameters for the LD LASSO. It returns three solutions, the fused, cp-optimal, and unfused solutions. It also creates a matrix of solutions needed for creating the trace plot.

Usage

ld_lasso_method(block.obj, block.cood = NA, Xa = NA, Y = NA, bpmap = NA, maxcol = 5e3, p.frac = 0.10, B = 5, s2low = 5e-3, s2high = 5e1, s2.vec.length = 4, null = FALSE)

Arguments

block.obj
An object of class gwaa.data from GenABEL.
block.cood
A vector of length p+1, where p is the number of SNPs. block.cood is an indicator vector that indicates block boundaries at all p+1 SNP bounded intervals. Use find.bounds to create this vector.
Xa
If block.obj is NA then a genotype matrix must be provided. Xa is a matrix of genotype values codes as 0, 1 or 2 for homozygous major, heterozygous, or homozygous minor, respectively.
Y
If block.obj is NA then a phenotype vector Y must be provided. Y is a vector of diagnoses, where 0 is non-diseased and 1 is diseased.
bpmap
A vector of map positions in terms of kB from the left boundary
maxcol
The upper limit on the number of columns in the constraint matrix. This is to prevent computational overload. Increasing maxcol may increase computation time and memory needed.
p.frac
The fraction of SNPs allowed in LASSO model under null hypothesis. This parameter is used in the function get.s1.
B
The number of bootstrap iterations for cp estimate.
s2low
The lower limit of the s2 vector
s2high
The upper limit of the s2 vector
s2.vec.length
The number of exponentially spaced values of s2.
null
A logical variable that indicates if analysis should be performed on permuted phenotype vector.

Value

beta1
The ld lasso solution with s2 that minimizes cp (cp-optimal solution)
beta2
The ld lasso solution for lower limit of s2 interval (fused solution)
beta3
The ld lasso solution for upper limit of s2 interval (unfused solution)
s2star
The s2 value that minimizes cp
cp.obj
A list that contains information used for cp estimation
log10p
A vector of log10 p values for test of allelic association
bpmap
A vector of map positions in base pairs
block.bounds.vec
A vector of block boundaries in kB from left boundary
s1
the LASSO constraint
B
Number of bootstrap samples
s2.vec.length
The length of the s2 vector

Details

Use function find.bounds to create block.cood vector with MATILDE MCMC methods. See ldlasso help page for details on the package MATILDE.

References

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

See Also

ld_lasso

Examples

Run this code
  # Load example data
  # data(ldlasso_example)
  
  # Run the method with low B and s2.vec.length first to test.
  # ldlasso.obj <- ld_lasso_method( block.obj, block.cood, B = 3, s2.vec.length = 2 )

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