ldlasso: LD LASSO Regression for SNP Association Study

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

Author
Samuel G. Younkin
Date of publication
2013-01-03 08:23:20
Maintainer
Samuel G. Younkin <samuel.younkin@gmail.com>
License
GPL (>= 2)
Version
3.2

View on CRAN

Man pages

block.bounds
Creates a vector of haplotype block boundary basepair...
block.cood
Vector of Haplotype Block Boundaries
block.map.matrix
Creates an indicator matrix for haplotype block boundaries,...
block.obj
GenABEL Object with Genotype and Phenotype Data
chi2
Creates a vector of chi-squared values from the allelic test...
get.cp
Uses bootstrap sampling over a vector of LD LASSO constraint...
get.s1
Finds an estimate for s1 based on an estimate of the expected...
heatmap
Plots the heat map for the LD LASSO solution space
ld_lasso
The main function of the LD LASSO method
ld_lasso_method
The LD LASSO function
ldlasso.obj
LD LASSO Object created by the function ld_lasso_method
ldlasso-package
LD LASSO for Case Control Genetic Association Study
p0tos1
Finds the LASSO parameter s1 that corresponds to desired...
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
trace.plot
Creates a trace plot for the LD LASSO

Files in this package

ldlasso
ldlasso/MD5
ldlasso/man
ldlasso/man/r2.cut.fn.Rd
ldlasso/man/chi2.Rd
ldlasso/man/block.obj.Rd
ldlasso/man/heatmap.Rd
ldlasso/man/plot_beta.Rd
ldlasso/man/plot_ldlasso.Rd
ldlasso/man/ld_lasso.Rd
ldlasso/man/block.cood.Rd
ldlasso/man/get.s1.Rd
ldlasso/man/block.map.matrix.Rd
ldlasso/man/ldlasso.obj.Rd
ldlasso/man/trace.plot.Rd
ldlasso/man/get.cp.Rd
ldlasso/man/block.bounds.Rd
ldlasso/man/p0tos1.Rd
ldlasso/man/ld_lasso_method.Rd
ldlasso/man/ldlasso-package.Rd
ldlasso/R
ldlasso/R/chi2.R
ldlasso/R/plot_ldlasso.R
ldlasso/R/plot_beta.R
ldlasso/R/block.map.matrix.R
ldlasso/R/ld_lasso.R
ldlasso/R/get.cp.R
ldlasso/R/ld_lasso_method.R
ldlasso/R/block.bounds.R
ldlasso/R/p0tos1.R
ldlasso/R/trace.plot.R
ldlasso/R/r2.cut.fn.R
ldlasso/R/get.s1.R
ldlasso/R/heatmap.R
ldlasso/doc
ldlasso/doc/ldlasso_vignette.pdf
ldlasso/DESCRIPTION
ldlasso/data
ldlasso/data/ldlasso_example.RData
ldlasso/NAMESPACE