LD LASSO Regression for SNP Association Study

Documentation for package ‘ldlasso’ version 3.2

ldlasso-package	LD LASSO for Case Control Genetic Association Study
block.bounds	Creates a vector of haplotype block boundary basepair positions.
block.cood	Vector of Haplotype Block Boundaries
block.map.matrix	Creates an indicator matrix for haplotype block boundaries, for use in ld_lasso.
block.obj	GenABEL Object with Genotype and Phenotype Data
blockcood	Vector of Haplotype Block Boundaries
blockobj	GenABEL Object with Genotype and Phenotype Data
chi2	Creates a vector of chi-squared values from the allelic test of association
get.cp	Uses bootstrap sampling over a vector of LD LASSO constraint parameters, s2, to compute a vector of cp estimates.
get.s1	Finds an estimate for s1 based on an estimate of the expected false positive rate. This function is a wrapper for p0tos1.
heatmap	Plots the heat map for the LD LASSO solution space
ldlasso	LD LASSO for Case Control Genetic Association Study
ldlasso.obj	LD LASSO Object created by the function ld_lasso_method
ldlassoobj	LD LASSO Object created by the function ld_lasso_method
ld_lasso	The main function of the LD LASSO method
ld_lasso_method	The LD LASSO function
p0tos1	Finds the LASSO parameter s1 that corresponds to desired false positive rate
plot_beta	Plot the LD LASSO solution by physical position.
plot_ldlasso	Diagnostic plot for an ldlasso object
plot_ld_lasso	Diagnostic plot for an ldlasso object
plot_ld_lasso_method	Diagnostic plot for an ldlasso object
r2.cut.fn	Find the r-squared cutoff
trace.plot	Creates a trace plot for the LD LASSO