Combine lists in forloop - r

Question

I have a list of chromosomes chromosomes <- c(1:2, "X", "Y") that I am iterating over to generate random data n times for each chromosome.
I am doing this first by iterating over the chromosomes and generating the data using generateData() and then adding these to a list which I then combine into a data frame outside of the loop using bp_data <- as.data.frame(do.call(rbind, simByChrom)):
chromosomes <- c(1:2, "X", "Y")
simByChrom <- list()
for (c in chromosomes){
n <- sample(1:5,1)
cat(paste("Simulating", n, "breakpoints on chromosome", c), "\n")
bp_data <- generateData(c, n)
simByChrom[[c]] <- bp_data
}
bp_data <- as.data.frame(do.call(rbind, simByChrom))
rownames(bp_data) <- NULL
# generate dummy data
generateData <- function(c, n){
df <- data.frame(chrom = rep(c, n),
pos= sample(1:10000, n))
return(df)
}
chrom pos
1 1 7545
2 2 5798
3 2 3863
4 3 4036
5 3 9347
6 3 4749
I would like to iterate over this multiple times and record the iteration number in bp_data$iteration, to produce a data frame that looks like this:
chrom pos iteration
1 7215 1
1 4606 1
2 8282 1
2 3501 1
2 4350 1
2 6044 1
X 2467 1
Y 2816 1
Y 8848 1
Y 2304 1
Y 4235 1
1 3760 2
1 8205 2
1 4735 2
2 3061 2
X 56 2
X 1722 2
X 2430 2
X 6749 2
X 2081 2
Y 9646 2
However, I'm unsure how to do this. I've tried:
iterations <- 2
for (i in (1:iterations)){
cat("Running iteration", i, "\n")
simByChrom <- list()
for (c in chromosomes){
n <- sample(1:5,1)
cat(paste("Simulating", n, "breakpoints on chromosome", c), "\n")
bp_data <- generateData(c, n)
bp_data$iteration <- i
simByChrom[[c]] <- bp_data
# or
# simByChrom[[c]][[i]] <- bp_data
# or
# simByChrom[[c]] <- bp_data
# simByChrom[[c]]$iteration <- i
}
bp_data <- as.data.frame(do.call(rbind, simByChrom))
rownames(bp_data) <- NULL
}
But this results in only the last iteration being recorded.
Can anyone suggest how I can achieve my desired result?

Answer 1

The reason you are only seeing the last iteration in your result is because bp_data is being over-written each time through the for loop. You need to make sure you save each iteration result separately and then combine them together at the end.
I believe just a few minor adjustments to what you already have will do the trick:
iterations <- 2
#create empty list to store each iteration result
bp_data <- list()
#run each iteration
for (i in 1:iterations){
cat("Running iteration", i, "\n")
simByChrom <- list()
for (c in chromosomes){
n <- sample(1:5,1)
cat(paste("Simulating", n, "breakpoints on chromosome", c), "\n")
aa <- generateData(c, n)
aa$iteration <- i
simByChrom[[c]] <- aa
}
result <- as.data.frame(do.call(rbind, simByChrom))
rownames(result) <- NULL
bp_data[[i]] <- result
}
#combine each iteration into one data frame
final <- as.data.frame(do.call(rbind, bp_data))