get_sdy: Get sd(y) from AF, n, b, se

In gap: Genetic Analysis Package

Get sd(y) from AF, n, b, se

Description

Get sd(y) from AF, n, b, se

Usage

get_sdy(f, n, b, se, method = "mean", ...)

Arguments

f	Allele frequency.
n	Sample size.
b	effect size.
se	standard error.
method	method of averaging: "mean" or "median".
...	argument(s) passed to method

Details

This function obtains standard error of a continuous outcome.

Value

sd(y).

Examples

## Not run: 
set.seed(1)
X1 <- matrix(rbinom(1200,1,0.4),ncol=2)
X2 <- matrix(rbinom(1000,1,0.6),ncol=2)
colnames(X1) <- colnames(X2) <- c("f1","f2")
Y1 <- rnorm(600,apply(X1,1,sum),2)
Y2 <- rnorm(500,2*apply(X2,1,sum),5)
summary(lm1 <- lm(Y1~f1+f2,data=as.data.frame(X1)))
summary(lm2 <- lm(Y2~f1+f2,data=as.data.frame(X2)))
b1 <- coef(lm1)
b2 <- coef(lm2)
v1 <- vcov(lm1)
v2 <- vcov(lm2)
require(coloc)
## Bayesian approach, esp. when only p values are available
abf <- coloc.abf(list(beta=b1, varbeta=diag(v1), N=nrow(X1), sdY=sd(Y1), type="quant"),
                 list(beta=b2, varbeta=diag(v2), N=nrow(X2), sdY=sd(Y2), type="quant"))
abf
# sdY
cat("sd(Y)=",sd(Y1),"==> Estimates:",sqrt(diag(var(X1)*b1[-1]^2+var(X1)*v1[-1,-1]*nrow(X1))),"\n")
for(k in 1:2)
{
  k1 <- k + 1
  cat("Based on b",k," sd(Y1) = ",sqrt(var(X1[,k])*(b1[k1]^2+nrow(X1)*v1[k1,k1])),"\n",sep="")
}
cat("sd(Y)=",sd(Y2),"==> Estimates:",sqrt(diag(var(X2)*b2[-1]^2+var(X2)*v2[-1,-1]*nrow(X2))),"\n")
for(k in 1:2)
{
  k1 <- k + 1
  cat("Based on b",k," sd(Y2) = ",sqrt(var(X2[,k])*(b2[k1]^2+nrow(X2)*v2[k1,k1])),"\n",sep="")
}
get_sdy(0.6396966,23991,0.04490488,0.009504684)

## End(Not run)

gap documentation built on Aug. 26, 2023, 5:07 p.m.