Permutation Test Exercises

The Exercises

We will use the following dataset to demonstrate the use of permutations:

url <- "https://raw.githubusercontent.com/genomicsclass/dagdata/master/inst/extdata/babies.txt"
filename <- basename(url)
download(url, destfile=filename)
babies <- read.table("babies.txt", header=TRUE)
bwt.nonsmoke <- filter(babies, smoke==0) %>% select(bwt) %>% unlist 
bwt.smoke <- filter(babies, smoke==1) %>% select(bwt) %>% unlist

1. We will generate the following random variable based on a sample size of 10 and observe the following difference:

N=10 
set.seed(1) 
nonsmokers <- sample(bwt.nonsmoke , N) 
smokers <- sample(bwt.smoke , N) 
obs <- mean(smokers) - mean(nonsmokers)

The question is whether this observed difference is statistically significant. We do not want to rely on the assumptions needed for the normal or t-distribution approximations to hold, so instead we will use permutations. We will reshuffle the data and recompute the mean. We can create one permuted sample with the following code:

dat <- c(smokers,nonsmokers)
shuffle <- sample(dat) 
smokersstar <- shuffle[1:N] 
nonsmokersstar <- shuffle[(N+1):(2*N)] 
mean(smokersstar)-mean(nonsmokersstar)

## [1] -8.5

The last value is one observation from the null distribution we will construct. Set the seed at 1, and then repeat the permutation 1,000 times to create a null distribution. What is the permutation derived p-value for our observation?

set.seed(1)
avgdiff <- replicate(1000, {
  dat <- c(smokers,nonsmokers)
  shuffle <- sample(dat) 
  smokersstar <- shuffle[1:N] 
  nonsmokersstar <- shuffle[(N+1):(2*N)]
  return(mean(smokersstar)-mean(nonsmokersstar))
})
hist(avgdiff)
abline(v=obs)

(sum(abs(avgdiff) > abs(obs)) + 1) / (length(avgdiff) + 1)

## [1] 0.05294705

2. Repeat the above exercise, but instead of the differences in mean, consider the differences in median obs <- median(smokers) - median(nonsmokers). What is the permutation based p-value?

set.seed(1)
avgdiff <- replicate(1000, {
  dat <- c(smokers,nonsmokers)
  shuffle <- sample(dat) 
  smokersstar <- shuffle[1:N] 
  nonsmokersstar <- shuffle[(N+1):(2*N)]
  return(median(smokersstar)-median(nonsmokersstar))
})
hist(avgdiff)
# mean observed difference
mean.p <- (sum(abs(avgdiff) > abs(obs)) + 1) / (length(avgdiff) + 1)
abline(v=obs, col = "blue")
# median observed difference
obs <- median(smokersstar)-median(nonsmokersstar)
median.p <- (sum(abs(avgdiff) > abs(obs)) + 1) / (length(avgdiff) + 1)
abline(v=obs, col = "red")

mean.p

## [1] 0.2827173

median.p

## [1] 0.3396603