Last data update: 2014.03.03
R: thresholds for two-stage gwas
twoStageNull R Documentation
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
Author(s)
Dirk F Moore <dirkfmoore@gmail.com>
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
Results