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ldlasso (version 3.2)

LD LASSO Regression for SNP Association Study

Description

ldlasso requires data be of class gwaa.data from the the package GenABEL

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Version

Install

install.packages('ldlasso')

Monthly Downloads

33

Version

3.2

License

GPL (>= 2)

Maintainer

Samuel G Younkin

Last Published

January 3rd, 2013

Functions in ldlasso (3.2)

p0tos1

Finds the LASSO parameter s1 that corresponds to desired false positive rate
block.bounds

Creates a vector of haplotype block boundary basepair positions.
block.obj

GenABEL Object with Genotype and Phenotype Data
trace.plot

Creates a trace plot for the LD LASSO
ldlasso.obj

LD LASSO Object created by the function ld_lasso_method
get.cp

Uses bootstrap sampling over a vector of LD LASSO constraint parameters, s2, to compute a vector of cp estimates.
ld_lasso

The main function of the LD LASSO method
ldlasso-package

LD LASSO for Case Control Genetic Association Study
block.cood

Vector of Haplotype Block Boundaries
heatmap

Plots the heat map for the LD LASSO solution space
block.map.matrix

Creates an indicator matrix for haplotype block boundaries, for use in ld_lasso.
get.s1

Finds an estimate for s1 based on an estimate of the expected false positive rate. This function is a wrapper for p0tos1.
chi2

Creates a vector of chi-squared values from the allelic test of association
plot_beta

Plot the LD LASSO solution by physical position.
plot_ldlasso

Diagnostic plot for an ldlasso object
r2.cut.fn

Find the r-squared cutoff
ld_lasso_method

The LD LASSO function