power.STEPS: power.STEPS

In WenjianBI/STEPS: Seoncdary Trait (ST) Analysis in Extreme Phenotype Sequencing (EPS)

Description

A function to calculate power for STEPS given a set of parameters

Usage

power.STEPS(maf, qntl = 0.1, N, b1, b3, g1)

Arguments

maf	minor allele frequency of SNP, between 0 and 0.5.
qntl	quantile to choose y1 and y2, between 0 and 0.5. Default value is 0.1, that is, subjects with primary phenotype of top 10% and bottom 10% are in cohort
N	sample size of dataset
b1	parameter to characterize association between genotype and primary trait. See 'Details' for more information.
b3	parameter to characterize association between secondary trait and primary trait. See 'Details' for more information.
g1	parameter to characterize association between genotype and secondary trait. See 'Details' for more information.

Details

For continuous secondary traits, model

Z = g0+g1*G+0.4*X+e1

Y = b0+b1*G+0.4*X+b3*Z+e2

For binary secondary traits, model

Z = g0+g1*G+0.4*X+e1

D = I(Z>cutoff)

Y = b0+b1*G+0.4*X+b3*Z+e2

where 'Z'/'D' is continuous/binary secondary trait, 'Y' is primary trait, 'X' is covariate following a standard normal distribution, 'G' is genotype following HWE with MAF of 'maf', error term 'e1'/'e2' follows a standard normal distribution, only subjects with primary phenotype at top/bottom quantile of 'qntl' are retained as extreme phenotype sampling design.

Value

An R data frame with powers for both continuous/binary traits and 4 significance levels from 1E-5 to 1E-8.

Examples

power.STEPS(maf=0.3,qntl=0.1,N=1000,b1=-0.4,b3=-0.7,g1=0.3)

WenjianBI/STEPS documentation built on July 22, 2019, 11:12 p.m.