ldlasso (version 3.2)

ldlasso.obj: LD LASSO Object created by the function ld_lasso_method

Description

This is a data frame created by the function ld_lasso_method. It contains information about the parameters used to generate the three LD LASSO solutions, as well as the solutions themselves. It also contains the results from the grid search performed to estimates the cp-optimal solution. (see cp.obj) Some basic map information is also stored here for use when plotting.

Usage

ldlasso.obj

Format

data.frame

beta1	numeric
cp-optimal solution	beta2
numeric	fused solution
beta3	numeric
un-fused solution	s2star
numeric	s2 parameter used for cp-optimal solution
cp.obj	data.frame
s2 and cp vectors along with solution matrix used to find s2star	log10p
numeric	log base 10 of p-values from allelic test of association for each SNP
bpmap	numeric
vector of physical SNP positions in kb from left boundary	block.bounds.vec
numeric	position of block boundaries in kb from left boundary (does not inlcude endpoints)
s1	numeric
LASSO parameter	B
numeric	number of bootstrap samples used by ld_lasso_method to find s2star
s2.vec.length	numeric
length of vector of s2 values used in ld_lasso_method	beta1

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