R: Uses bootstrap sampling over a vector of LD LASSO constraint...
get.cp
R Documentation
Uses bootstrap sampling over a vector of LD LASSO constraint parameters,
s2, to compute a vector of cp estimates.
Description
The vector of cp estimates is used to identify the cp-optimal solution.
Usage
get.cp(s2low, s2high, s2.vec.length, block.obj, Xa = NA, Y = NA, s1, r2.cut, block.cood, B = 20)
Arguments
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.
providing 
.