mthacases: Sample size calculations - mtDNA haplogroups

In aurora-mareviv/mthapower: Sample Size and Power for Association Studies Involving Mitochondrial DNA Haplogroups

Description

Determine the minimum number of cases (Ncmin), required to detect: either a change from p0 (haplogroup frequency in controls) to p1 (haplogroup frequency in cases), or a given OR, with a predefined confidence interval, in a study with Nh haplogroups. Note: I assume that case-control equations are valid for cohorts with a balanced number of cases and controls. This function may not be generalizable for all studies involving mtDNA haplogroups.

Usage

mthacases(p0 = p0, Nh = Nh, OR.cas.ctrl = OR.cas.ctrl,
  power = power, sig.level = sig.level)

Arguments

p0	the frequency of the haplogroup in the control population, (that is, the controls among exposed). It depends on haplogroup baseline frequency.
Nh	number of haplogroup categories. Usually 10 haplogroups plus one category for rare haplogroups: Nh <- 11.
OR.cas.ctrl	(p1 / (1-p1)) / (p0 / (1-p0)) the OR you want to detect with your data. It can be either a single value, or a sequence: OR.cas.ctrl <- 2; OR.cas.ctrl <- seq(1.25,3 by=0.5).
power	the power to detect a given OR in my study (usually 80-90).
sig.level	the alpha error accepted. Can take 3 possible values: 0.05, 0.01 and 0.001 (see [Table 2] of Samuels et al).

Value

Gives the result in a data frame, easy to print in a plot.

Author(s)

Author and maintainer: Aurora Baluja. Email: [e-mail]

References

1. DC Samuels, AD Carothers, R Horton, PF Chinnery. The Power to Detect Disease Associations with Mitochondrial DNA Haplogroups. AJHG, 2006. 78(4):713-720. DOI:10.1086/502682.

2. Source code: github.com/aurora-mareviv/mthapower.

3. Shiny app: aurora.shinyapps.io/mtDNA_power_calc.

Examples

mydata <- mthacases(p0=0.445, Nh=11,
                    OR.cas.ctrl=c(2), power=80,
                    sig.level=0.05) # Baudouin study
mydata <- mthacases(p0=0.445, Nh=11,
                    OR.cas.ctrl=c(1.25,1.5,1.75,2,2.25,2.5,2.75,3),
                    power=80, sig.level=0.05)
mydata <- mydata[c(2,6)]
mydata
plot(mydata)

aurora-mareviv/mthapower documentation built on June 24, 2019, 4:19 p.m.