genpwr
The genpwr package for R (>3.5.1) performs power and sample size calculations for genetic association studies and allows for mis-specification of the genetic model. Calculations can be performed for binary (case/control) and continuous outcomes. Power and sample size calculations are possible for genetic effects as well as gene by environment interactions.
Example
To calculate power to detect an odds ratio of 2 for a 1:1 case control study with 2,000 subjects, assuming an alpha of 0.05, at minor allele frequencies of 0.1, 0.2, and 0.3:
library(genpwr)
#> Loading required package: ggplot2
#> Loading required package: nleqslv
#> Loading required package: MASS
genpwr.calc(calc = "power", model = "logistic", N = 2000, OR = 2,
Alpha = 0.05, MAF = c(0.1,0.2,0.3), Case.Rate = 0.5)
#> Test.Model True.Model MAF OR N_total N_cases N_controls Case.Rate
#> 1 Dominant Dominant 0.1 2 2000 1000 1000 0.5
#> 3 Dominant Additive 0.1 2 2000 1000 1000 0.5
#> 5 Dominant Recessive 0.1 2 2000 1000 1000 0.5
#> 7 Dominant Dominant 0.2 2 2000 1000 1000 0.5
#> 9 Dominant Additive 0.2 2 2000 1000 1000 0.5
#> 11 Dominant Recessive 0.2 2 2000 1000 1000 0.5
#> 13 Dominant Dominant 0.3 2 2000 1000 1000 0.5
#> 15 Dominant Additive 0.3 2 2000 1000 1000 0.5
#> 17 Dominant Recessive 0.3 2 2000 1000 1000 0.5
#> 12 Recessive Dominant 0.1 2 2000 1000 1000 0.5
#> 31 Recessive Additive 0.1 2 2000 1000 1000 0.5
#> 51 Recessive Recessive 0.1 2 2000 1000 1000 0.5
#> 71 Recessive Dominant 0.2 2 2000 1000 1000 0.5
#> 91 Recessive Additive 0.2 2 2000 1000 1000 0.5
#> 111 Recessive Recessive 0.2 2 2000 1000 1000 0.5
#> 131 Recessive Dominant 0.3 2 2000 1000 1000 0.5
#> 151 Recessive Additive 0.3 2 2000 1000 1000 0.5
#> 171 Recessive Recessive 0.3 2 2000 1000 1000 0.5
#> 14 Additive Dominant 0.1 2 2000 1000 1000 0.5
#> 32 Additive Additive 0.1 2 2000 1000 1000 0.5
#> 52 Additive Recessive 0.1 2 2000 1000 1000 0.5
#> 72 Additive Dominant 0.2 2 2000 1000 1000 0.5
#> 92 Additive Additive 0.2 2 2000 1000 1000 0.5
#> 112 Additive Recessive 0.2 2 2000 1000 1000 0.5
#> 132 Additive Dominant 0.3 2 2000 1000 1000 0.5
#> 152 Additive Additive 0.3 2 2000 1000 1000 0.5
#> 172 Additive Recessive 0.3 2 2000 1000 1000 0.5
#> 16 2df Dominant 0.1 2 2000 1000 1000 0.5
#> 33 2df Additive 0.1 2 2000 1000 1000 0.5
#> 53 2df Recessive 0.1 2 2000 1000 1000 0.5
#> 73 2df Dominant 0.2 2 2000 1000 1000 0.5
#> 93 2df Additive 0.2 2 2000 1000 1000 0.5
#> 113 2df Recessive 0.2 2 2000 1000 1000 0.5
#> 133 2df Dominant 0.3 2 2000 1000 1000 0.5
#> 153 2df Additive 0.3 2 2000 1000 1000 0.5
#> 173 2df Recessive 0.3 2 2000 1000 1000 0.5
#> Power_at_Alpha_0.05
#> 1 0.99997130
#> 3 0.99999117
#> 5 0.06094645
#> 7 0.99999997
#> 9 1.00000000
#> 11 0.12562959
#> 13 0.99999999
#> 15 1.00000000
#> 17 0.26400143
#> 12 0.23736708
#> 31 0.72802319
#> 51 0.32261174
#> 71 0.51913618
#> 91 0.99712300
#> 111 0.84110046
#> 131 0.65907220
#> 151 0.99999669
#> 171 0.99128361
#> 14 0.99994745
#> 32 0.99999535
#> 52 0.09704782
#> 72 0.99999973
#> 92 1.00000000
#> 112 0.39542984
#> 132 0.99999976
#> 152 1.00000000
#> 172 0.83339405
#> 16 0.99987562
#> 33 0.99997633
#> 53 0.24913314
#> 73 0.99999976
#> 93 1.00000000
#> 113 0.75849311
#> 133 0.99999996
#> 153 1.00000000
#> 173 0.97950882"The return object contains information about power for additive, dominant, recessive, and 2df / genotypic tests of association, assuming various true underlying genetic effects (additive, dominant, recessive). "
Installation instructions
To install genpwr, perform the following steps:
- Install R version 3.5.1 or higher by following the instructions at https://www.R-project.org
- From the R environment, install and load the "genpwr" package:
install.packages("genpwr")- Load the library
library(genpwr)Demo
Install the genpwr package as described above.
Run the genpwr demo program
demo(genpwr_demo)