Haplin (version 7.3.2)

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)

Value

hapPower returns the simulated power.

Arguments

hapRun.result

The result of running hapRun

alpha

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

Author

Miriam Gjerdevik,
with Hakon K. Gjessing
Professor of Biostatistics
Division of Epidemiology
Norwegian Institute of Public Health

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 https://haplin.bitbucket.io/docu/Haplin_power.pdf.

References

Web Site: https://haplin.bitbucket.io

See Also

haplin, haplinSlide, hapSim, hapRun, snpPower, snpSampleSize , hapPowerAsymp

Examples

if (FALSE) {
## 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.res <- 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", ask = FALSE)
hapPower(hapRun.res)

## 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.res <- 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 = TRUE, 
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 = TRUE, hapfunc = "haplinStrat", n.sim = 100, ask = FALSE)
hapPower(hapRun.res)

## Simulate power at the 0.1 significance level from 1000 files using haplin.
## The files consist of fetal effects at one diallelic locus,
## corresponding to haplo.freq = c(0.1,0.9), RR = c(2,1) and RRstar = c(1,1).
## The data consists of a combination of 100 case triads and 100 control triads.
hapRun.res <- 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, ask = FALSE)
hapPower(hapRun.res, 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)
}