Returns the minimum value of r2 in r2.vec that keeps the number of constraint matrix columns less than maxcol.
● Data Source:
CranContrib
● Keywords:
● Alias: r2.cut.fn
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One degree of freedom Chi-squared test of allelic counts
● Data Source:
CranContrib
● Keywords:
● Alias: chi2
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This function uses the matrix beta0.mat, computed by the function ld_lasso_method, to plot a heat map of LD LASSO solutions. Increasing darkness corresponds to increasing values for the SNP LD LASSO estimate.
● Data Source:
CranContrib
● Keywords:
● Alias: heatmap
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Creates a plot of LD LASSO estimates using the physical map, bpmap
● Data Source:
CranContrib
● Keywords:
● Alias: plot_beta
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Creates four plots; Top-left: Allelic test of association; Top- right: cp-optimal, fused, and unfused solutions (black, red, green); Bottom-left: Trace plot with fixed s1 ; Bottom-right: cp estimates vs. s2
● Data Source:
CranContrib
● Keywords:
● Alias: plot_ld_lasso, plot_ld_lasso_method, plot_ldlasso
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ld_lasso
(Package: ldlasso) :
The main function of the LD LASSO method
The LD LASSO uses the correlation of SNP genotypes in a penalized least squares regression framework. The estimator is the solution to a convex optimization problem, and here we use the solution from the package quadprog.
● Data Source:
CranContrib
● Keywords:
● Alias: ld_lasso
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This function calls the function p0tos1, which finds an estimate for s1, given p0, where p0 is the number of nonzero estimates found with a permuted phenotype vector.
● Data Source:
CranContrib
● Keywords:
● Alias: get.s1
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block.map.matrix
(Package: ldlasso) :
Creates an indicator matrix for haplotype block boundaries, for
Simple function that maps the block boundary vector to an indicator matrix for use in the definition of constraint matrix. This matrix ensures that only within block SNP pairs are considered.
● Data Source:
CranContrib
● Keywords:
● Alias: block.map.matrix
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This function creates a trace plot as a function of s2, the LD LASSO constraint
● Data Source:
CranContrib
● Keywords:
● Alias: trace.plot
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The vector of cp estimates is used to identify the cp-optimal solution.
● Data Source:
CranContrib
● Keywords:
● Alias: get.cp
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