ratiometricBinomPoweredEffectSize: Calculates the effect size of a driver gene according to a...

In KarchinLab/cancerSeqStudy: Power and False Positive Analysis of Cancer Sequencing Studies

Description

Effect size is measures as the fraction of sample/patient cancers with a mutation in a driver gene above the background mutation rate.

Usage

ratiometricBinomPoweredEffectSize(possible.effect.sizes, desired.power, p, mu,
  samp.size, Df = 1, signif.level = 5e-06, Leff = 1500 * 3/4)

Arguments

possible.effect.sizes	vector of effect sizes
desired.power	A floating point number indicating desired power
p	the background fraction of total mutations represented by the ratio-metric feature (e.g. inactivating mutations / total)
mu	Mutation rate per base
samp.size	number of cancer samples in study
Df	fraction of driver mutations that are the specific one of interest
signif.level	significance level for binomial test
Leff	effective gene length of CDS in bases for an average gene

Value

List containing the smallest effect size with sufficient power

KarchinLab/cancerSeqStudy documentation built on May 8, 2019, 4:47 p.m.