twoStageNull: thresholds for two-stage gwas
In twoStageGwasPower: Compute thresholds and power for two-stage gwas

Description Usage Arguments Value Author(s) References Examples

View source: R/twoStageNull.R

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

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

`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

A list containing:

`c1`	Stage one threshold
`c2`	Replication (stage two) threshold
`c.joint`	Joint analysis threshold
`c.singleStage`	Single stage design threshold

Dirk F Moore <dirkfmoore@gmail.com>

Skol AD, Scott, LJ, Abecasis GR, Boehnke M (2006) Nature Genetics doi:10.1038/ng1706

http://www.sph.umich.edu/csg/abecasis/CaTS/

# 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