twoStageGwasPower (version 0.99.0)

twoStageNull: thresholds for two-stage gwas

Description

Computes thresholds for two-stage genome-wide association study for replication and joint analyses, and for a single-stage design

Usage

twoStageNull(pi.samples, pi.markers, alpha.marker)

Arguments

pi.samples

Proportion of samples genotyped in Stage 1

pi.markers

Proportion of markers genotyped in Stage 2

alpha.marker

Significance level used for each marker, accounting for multiple comparisons among a large number of markers

Value

A list containing:

c1

Stage one threshold

c2

Replication (stage two) threshold

c.joint

Joint analysis threshold

c.singleStage

Single stage design threshold

References

Skol AD, Scott, LJ, Abecasis GR, Boehnke M (2006) Nature Genetics doi:10.1038/ng1706 http://www.sph.umich.edu/csg/abecasis/CaTS/

Examples

# compute thresholds for two-stage design with 40% of subjects selected for stage one
#  and 10% of markers selected for follow-up in the second stage,
#  with an alpha level of 0.05/300000
power.thresh.out <- twoStageNull(pi.samples=0.40, pi.markers=0.10, 
                                 alpha.marker=0.05/300000)
power.thresh.out