ldlasso (version 3.2)

get.s1: 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.

Value

Given the number of nonzero SNPs allowed with permuted phenotype vector, p0, this function returns an estimate for s1.

Details

This function increases the value for p0 if NA is returned from p0tos1. The bisection algorthim is contained in the function p0tos1

See Also

p0tos1