Last data update: 2014.03.03

 R: LD LASSO Object created by the function ld_lasso_method
ldlasso.objR Documentation

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

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

Results


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO