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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
Version
3.2
3.1
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Install
install.packages('ldlasso')
Monthly Downloads
17
Version
3.2
License
GPL (>= 2)
Maintainer
Samuel G Younkin
Last Published
January 3rd, 2013
Functions in ldlasso (3.2)
Search functions
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