Returns the minimum value of r2 in r2.vec that keeps the number of constraint matrix columns less
than maxcol.
Usage
r2.cut.fn(block.obj, block.cood, Xa, Y, maxcol, r2.cut.min, r2.cut.max, r2.vec.length)
Arguments
block.obj
An object of class gwaa.data from GenABEL.
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.
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.
maxcol
The maximum number of columns allowed in the constraint matrix. Default is 5,000.
r2.cut.min
The lower bound of the r2.cut interval
r2.cut.max
The upper bound of the r2.cut interval
r2.vec.length
The number of r2.cut values uniformly spaced in r2.cut interval
Value
The function r2.cut.fn returns the minimum value of r2.cut that satsisfies, ncol(A) < maxcol, where A is the constraint matrix