powerEQTL.sLR: Power Calculation for EQTL Analysis Based on Simple Linear...

In sterding/powerEQTL: Power and Sample Size Calculation for eQTL Analysis

Description

Power calculation for eQTL analysis that tests if a SNP is associated to a gene probe by using simple linear regression.

Usage

powerEQTL.SLR(
  MAF,
  typeI = 0.05,
  nTests = 2e+05,
  slope = 0.13,
  myntotal = 200,
  mystddev = 0.13,
  verbose = TRUE)

Arguments

MAF	Minor allele frequency.
typeI	Type I error rate for testing if a SNP is associated to a gene probe.
nTests	integer. Number of tests in eQTL analysis.
slope	Slope beta_1 of the simple linear regression y_i = beta_0 + beta_1 * x_i + epsilon_i, where y_i is the gene expression level of the i-th subject, x_i is the genotype of the i-th subject, and epsilon_i is the random error term. Additive coding for genotype is used.
myntotal	integer. Number of subjects.
mystddev	Standard deviation of the random error term epsilon in simple linear regression.
verbose	logic. indicating if intermediate results should be output.

Details

To test if a SNP is associated with a gene probe, we use the simple linear regression

y_i = beta_0 + beta_1 * x_i + epsilon_i,

where y_i is the gene expression level of the i-th subject, x_i is the genotype of the i-th subject, and ε_i is the random error term. Additive coding for genotype is used. To test if the SNP is associated with the gene probe, we test the null hypothesis H_0: beta_1 = 0.

Denote p as the minor allele frequency (MAF) of the SNP. Under Hardy-Weinberg equilibrium, we can calculate the variance of genotype of the SNP: sigma^2_x = 2 * p * (1 - p), where sigma^2_x is the variance of the predictor (i.e. the SNP) x_i.

We then can use Dupont and Plummer's (1998) power/sample size calculation formula to calculate the minimum detectable slope, adjusting for multiple testing.

Value

power of the test after Bonferroni correction for multiple testing.

Author(s)

Xianjun Dong <[e-mail]>, Tzuu-Wang Chang <[e-mail]>, Scott T. Weiss <[e-mail]>, Weiliang Qiu <[e-mail]>

References

Dupont, W.D. and Plummer, W.D.. Power and Sample Size Calculations for Studies Involving Linear Regression. Controlled Clinical Trials. 1998;19:589-601.

See Also

ssEQTL.SLR, minSlopeEQTL.SLR

Examples

powerEQTL.SLR(
  MAF = 0.1,
  typeI = 0.05,
  nTests = 2e+05,
  slope = 0.13,
  myntotal = 176,
  mystddev = 0.13,
  verbose = TRUE)

sterding/powerEQTL documentation built on May 30, 2019, 4:42 p.m.