Haplin (version 6.0.1)

hapPower: Power simulation for association analyses with Haplin

Description

Simulates the statistical power of genetic analyses assessing fetal effects, maternal effects and/or parent-of-origin effects. Effects of X-chromosome genes and gene-environment interaction effects are also allowed.

Usage

hapPower(hapRun.result, alpha = 0.05)

Arguments

hapRun.result

The result of running hapRun

alpha

alpha is the Type I Error probablity. Equals 0.05 by default.

Value

returns the simulated power.

Details

The Haplin framework includes different modules for assessing genetic effects: haplin, haplinStrat and haplinSlide. hapPower simulates the power of these analyses, which enables power calculations of fetal effects, maternal effects and/or parent-of-origin effects. Various family designs, i.e., triads, case-control, the hybrid design, and all intermediate designs, are possible. It also allows power calculation of gene-environment interaction effects and effects on X-chromosome markers.

hapPower calculates statistical power using the result of hapRun, and the target effects must be specified in this function, see Examples below, and details in http://folk.uib.no/gjessing/genetics/software/haplin/Haplin_power.pdf.

References

Web Site: http://folk.uib.no/gjessing/genetics/software/haplin/

See Also

haplin, haplinSlide, hapSim, hapRun, snpPower

Examples

## Not run: 
# 
# ## Simulate power from 100 files using haplin. 
# ## The files consist of fetal effects at two diallelic markers,
# ## corresponding to haplo.freq = rep(0.25, 4), RR = c(2,1,1,1) and RRstar = c(1,1,1,1).
# ## The power is simulated for the combination of 100 case triads 
# ## and 100 control triads with no missing data at a 0.05 significance level,
# ## applying a multiplicative model.
# .hapRun <- hapRun(nall = c(2,2), n.strata = 1, cases = c(mfc=100), controls = c(mfc=100),
# haplo.freq = rep(0.25,4), RR = c(2,1,1,1), RRstar = c(1,1,1,1), 
# hapfunc = "haplin", response = "mult", n.sim = 100, dire = "simfiles")
# hapPower(.hapRun)
# 
# ## Simulate power from 100 files applying haplinStrat. 
# ## The files consist of fetal and maternal effects at two diallelic markers.
# ## The data is simulated for 500 case triads and 200 control families in the first stratum,
# ## and 500 case triads and 500 control trids in the second.
# ## The fetal effects vary across strata,
# ## whereas the maternal effects are the same.
# ## One percent of the case triads are missing at random in the second stratum.
# .hapRun <- hapRun(nall = c(2,2), n.strata = 2, cases = c(mfc=500),
# controls = list(c(mfc=200),c(mfc=500)), haplo.freq = rep(0.25,4), maternal = T, 
# RR = list(c(1.5,1,1,1),c(1,1,1,1)), RRstar = c(1,1,1,1),
# RR.mat = c(1.5,1,1,1), RRstar.mat = c(1,1,1,1), gen.missing.cases = list(NULL,0.01), 
# use.missing = T, hapfunc = "haplinStrat", n.sim = 100)
# hapPower(.hapRun)
# 
# ## Simulate power at the 10
# ## The files consist of fetal effects at one diallelic locus,
# ## corresponding to haplo.freq = c(0.1,0.9), RR = c(1.5,1) and RRstar = c(1,1).
# ## The data consists of a combination of 100 case triads and 100 control triads.
# .hapRun <- hapRun(nall = c(2), cases = c(mfc=100), controls = c(mfc=100),
# haplo.freq = c(0.1,0.9), RR = c(2,1), RRstar = c(1,1),
# hapfunc = "haplin", response = "mult", n.sim = 1000)
# hapPower(.hapRun, alpha= 0.10)
# 
# ## The latter example, applying response = "mult", should be comparable to 
# ## the theoretic calculations of snpPower.
# snpPower(cases = list(mfc=100), controls = list(mfc=100),
# RR = 2, MAF = 0.1, alpha = 0.10)
# ## End(Not run)