Description Usage Arguments Details Value Author(s) See Also
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.
1 |
i |
Number of nonzero estimates in permuted model. If the expected false positive rate is desired to be 0.10, then set i = 0.10*p, where p is the number of SNPs. |
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. |
r2.cut |
Value for the cutoff value of r-squared. Can be found with r2.cut.fn. |
s1high |
The initial upper limit in the bisection algorithm |
s1low |
The lower upper limit in the bisection algorithm |
max.iter |
The maximum number of iterations allowed in the bisection algorithm before NA is returned |
tol |
If p never equals i the bisection algorithim stops when |s1.old - s1.new| < tol. Otherwise algortithm stops when p = i. |
This function increases the value for p0 if NA is returned from p0tos1. The bisection algorthim is contained in the function p0tos1
Given the number of nonzero SNPs allowed with permuted phenotype vector, p0, this function returns an estimate for s1.
Samuel G. Younkin
p0tos1
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