GASpower

R implementation of the Genomic Association Study (GAS) Power Calculator.

Calculates statistical power for genomic association studies. Based on Genomic Association Study (GAS) Power Calculator Copyright 2017, Jennifer Li Johnson, University of Michigan School of Public Health. doi: https://doi.org/10.1101/164343

Install instructions

Install with the commands:

install.packages("remotes")
remotes::install_github("JamesR-S/GASpower")

Usage

Calculate Power

GAS_power_calc(daf,grr,prevalence,cases,controls,alpha,model)

Arguments:

• daf - disease allele frequency: frequency of the disease risk allele in the general population.
• grr - genotype relative risk.
• prevalence - general population disease prevelance: probability that a randomly sampled individual has the disease. If prevalence is not provided then it will be calculated based on the case and control numbers.
• cases - n cases in study.
• controls - n controls in study.
• alpha - desired significance level (alpha).
• model - disease model: can be any of "multiplicative","additive","dominant","recessive".

Example

GAS_power_calc(0.5000,1.5,0.1,1000,1000,0.000007,"multiplicative")

Plot Power

GAS_power_plot(plot_variable,from,to,by,daf,grr,prevalence,cases,controls,alpha,model)

Arguments:

• plot_variable - choice of variable for power to be plotted against. This variable does not need to be defined later in the function.
• from - start value for plot variable
• to - end value for plot variable
• by - step size for plot variable
• daf - disease allele frequency: frequency of the disease risk allele in the general population.
• grr - genotype relative risk.
• prevalence - general population disease prevelance: probability that a randomly sampled individual has the disease. If prevalence is not provided then it will be calculated based on the case and control numbers.
• cases - n cases in study.
• controls - n controls in study.
• alpha - desired significance level (alpha).
• model - disease model: can be any of "multiplicative","additive","dominant","recessive".

Example

GAS_power_plot("grr",from = 1, to = 10, by = 0.5,daf=0.0000005,cases=39000,controls=36000,alpha = 0.05,model="dominant")