R: Finds an estimate for s1 based on an estimate of the expected...
get.s1
R Documentation
Finds an estimate for s1 based on an estimate of the expected false positive
rate. This function is a wrapper for p0tos1.
Description
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.
Usage
get.s1(i, block.obj, Xa = NA, Y = NA, r2.cut, s1high, s1low, max.iter, tol)
Arguments
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.
Details
This function increases the value for p0 if NA is returned from
p0tos1. The bisection algorthim is contained in the function p0tos1
Value
Given the number of nonzero SNPs allowed with permuted phenotype
vector, p0, this function returns an estimate for s1.
providing 
.