Sample size for family-based linkage and association design
This function implements Risch and Merikangas (1996) statistics evaluating power for family-based linkage (affected sib pairs, ASP) and association design. They are potentially useful in the prospect of genome-wide association studies.
The function calls auxiliary functions sn() and strlen; sn() contains the necessary thresholds for power calculation while strlen() evaluates length of a string (generic).
fbsize(gamma,p,alpha=c(1e-4,1e-8,1e-8),beta=0.2,debug=0,error=0)
gamma |
genotype relative risk assuming multiplicative model |
p |
frequency of disease allele |
alpha |
Type I error rates for ASP linkage, TDT and ASP-TDT |
beta |
Type II error rate |
debug |
verbose output |
error |
0=use the correct formula,1=the original paper |
The returned value is a list containing:
gamma |
input gamma |
p |
input p |
n1 |
sample size for ASP |
n2 |
sample size for TDT |
n3 |
sample size for ASP-TDT |
lambdao |
lambda o |
lambdas |
lambda s |
Risch, N. and K. Merikangas (1996). The future of genetic studies of complex human diseases. Science 273(September): 1516-1517.
Risch, N. and K. Merikangas (1997). Reply to Scott el al. Science 275(February): 1329-1330.
Scott, W. K., M. A. Pericak-Vance, et al. (1997). Genetic analysis of complex diseases. Science 275: 1327.
extracted from rm.c
Jing Hua Zhao
models <- matrix(c(
4.0, 0.01,
4.0, 0.10,
4.0, 0.50,
4.0, 0.80,
2.0, 0.01,
2.0, 0.10,
2.0, 0.50,
2.0, 0.80,
1.5, 0.01,
1.5, 0.10,
1.5, 0.50,
1.5, 0.80), ncol=2, byrow=TRUE)
outfile <- "fbsize.txt"
cat("gamma","p","Y","N_asp","P_A","H1","N_tdt","H2","N_asp/tdt","L_o","L_s\n",
file=outfile,sep="\t")
for(i in 1:12) {
g <- models[i,1]
p <- models[i,2]
z <- fbsize(g,p)
cat(z$gamma,z$p,z$y,z$n1,z$pA,z$h1,z$n2,z$h2,z$n3,z$lambdao,z$lambdas,file=outfile,
append=TRUE,sep="\t")
cat("\n",file=outfile,append=TRUE)
}
table1 <- read.table(outfile,header=TRUE,sep="\t")
nc <- c(4,7,9)
table1[,nc] <- ceiling(table1[,nc])
dc <- c(3,5,6,8,10,11)
table1[,dc] <- round(table1[,dc],2)
unlink(outfile)
# APOE-4, Scott WK, Pericak-Vance, MA & Haines JL
# Genetic analysis of complex diseases 1327
g <- 4.5
p <- 0.15
cat("\nAlzheimer's:\n\n")
fbsize(g,p)
# note to replicate the Table we need set alpha=9.961139e-05,4.910638e-08 and
# beta=0.2004542 or reset the quantiles in fbsize.RPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.