Description Usage Arguments Value Author(s) See Also
The vector of cp estimates is used to identify the cp-optimal solution.
1 | get.cp(s2low, s2high, s2.vec.length, block.obj, Xa = NA, Y = NA, s1, r2.cut, block.cood, B = 20)
|
s2low |
The lower limit for the s2 vector. |
s2high |
The upper limit for the s2 vector. |
s2.vec.length |
The number of exponentially spaced values in the s2 vector. |
block.obj |
An object of class gwaa.data from GenABEL. |
Xa |
If block.obj is NA then a genotype matrix must be provided. Xa is a matrix of genotype values codes as 0, 1 or 2 for homozygous major, heterozygous, or homozygous minor, respectively. |
Y |
If block.obj is NA then a phenotype vector Y must be provided. Y is a vector of diagnoses, where 0 is non-diseased and 1 is diseased. |
s1 |
The LASSO parameter |
r2.cut |
Only SNP pairs with correlation greater than r2.cut are bounded by the LD LASSO constraint. |
block.cood |
A vector of length p+1, where p is the number of SNPs. block.cood is an indicator vector that indicates block boundaries at all p+1 SNP bounded intervals. Use find.bounds to create this vector. |
B |
Number of bootstrap samples |
s2.vec |
A vector of s2 values |
cp.vec |
A vector of cp estimates |
beta0.mat |
A matrix of LD LASSO estimates |
s1 |
The LASSO parameter |
Samuel G. Younkin
ld_lasso_method
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