Function to append elements to a list only if they exist

I've created this function that puts together a list from object names, but can handle when the object doesn't exist. The function works fine on its own, but when I try and call it within another function I just get NA out for each list element. What's going on? Here's a simplified example:

genes <- c("gene1", "gene2", "gene3", "gene4")
analyses <- c("analysis_one", "analysis_two")

# Function to put together a list even if an element doesn't exist
append_if_exists <- function(element_names) {
  
  # Create empty list
  my_list <- list()
  
  # Get and append each new element
  for (element_name in element_names) {
    
    # Get new element
    if (exists(element_name)) {
      element <- list(get(element_name))
      names(element) <- element_name
    } else {
      element <- list(NA)
      names(element) <- element_name
    }
    
    # Append new element
    my_list <- c(my_list, element)
    
  }
  
  # Output
  return(my_list)
  
}

my_function <- function(genes, analyses) {
  
  # Analysis one
  if ("analysis_one" %in% analyses) {
    output1 <- genes[1:3]
  }
  
  # Analysis two
  if ("analysis_two" %in% analyses) {
    output2 <- genes[1:2]
  }
  
  # Append if exists
  out <- append_if_exists(c("output1", "output2"))
  return(out)
  
}

# Run the function and my list has the right names, but the elements are just 'NA'
result <- my_function(genes, analyses)

# Run the same thing outside of the function and it works fine!
output1 <- genes[1:3]
output2 <- genes[1:2]
result <- append_if_exists(c("output1", "output2"))

Rather than write your own append_if_exists, just use the built in mget() function. If you want to avoid names that don't exist, intersect the names with the names in the current scope. This should work

my_function <- function(genes, analyses) {
  ...

  out <- mget(intersect(c("output1", "output2"), ls()))
  return(out)
}

The problem with your solution is that you need to pay attention to the environment where objects are found. R uses lexical scoping, so functions resolve variables in the environment where the function was defined, not where it was called. If you define append_if_exists in the global environment, then it can't see output1 and output2 which are defined in the my_function runtime environment. The get() function does have an envir= parameter so you could pass in the appropriate environment to the function but that would get messy quickly.