How to index R objects within a for loop?

Question

I'm trying to use a for loop to simplify the following code:

a1 <- CreateSeuratObject (raw.data = a1.data)
a2 <- CreateSeuratObject (raw.data = a2.data)
a3 <- ...

I've tried the following:

samples <- c("a1", "a2", "a3")
samples.data <- c("a1.data", "a2.data", "a3.data")
for (i in samples) {
  for (j in samples.data) {
    i <- CreateSeuratObject(raw.data = j)    
  }
}

But it returns the following error:

Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 
 'x' must be an array of at least two dimensions

The CreateSeuratObject function essentially tries to read the samples.data vector instead of indexing the corresponding item in the vector. How can I fix this?

Answer 1

Here are three ways of doing what you want. I suggest you do not use the first way.

samples <- c("a1", "a2", "a3")
samples.data <- c("a1.data", "a2.data", "a3.data")

for (i in seq_along(samples)) {
    assign(samples[i], CreateSeuratObject(raw.data = samples.data[i]))
}

samples_list <- vector("list", length = length(samples))
for (i in seq_along(samples)) {
  samples_list[[i]] <- CreateSeuratObject(raw.data = samples.data[i]))
}
names(samples_list) <- samples

samples_list2 <- lapply(samples.data, CreateSeuratObject)
names(samples_list2) <- samples