I have 50 text files all beginning with NEW. I want to loop through each textfile/dataframe and run the same functions for each of these files and then output the results via the write.table function. Therefore, for each 50 files, the same functions are applied and then 50 independent output results should be created containing the original name with word 'output' at the end.

Here is my code. I have used the list.file function to read in the 50 files but how can I adapt my code below so that each of the below R commands/functions run for each of the 50 files independently and then output the corresponding 50 files?

file_list <- list.files("/data/genome/relevantfiles/AL/*NEW*.")  #reading in the list of 50 files in my directory all starting with NEW


df <- file_list  #each file *NEW* is a df #this does not work - how can apply each file into a dataframe.

##code for each dataframe. The code/function is shown more simply below because it works 

#running a function on the dataframe
df_output_results <- coloc.susie(dataset1 = list(beta=df$BETA, varbeta=df$Varbeta, N=1597, type="quant" ...)

#printing out results for each dataframe
final_results <- print(df_output_results$summary)

#outputting results 
write.table(final_results, file = paste0(fileName,"_output.txt"), quote = F, sep = "\t")

I am unsure how to adapt the code so that each file is inputted in a list and the following R codes are applied to each file in the code block and then outputted into a seperate file ... repeated for 50 files. I am assuming I need to use lapply but not sure how to use this? The codes in the code block work so there is not issue with the codes.

CodePudding user response：

From what I understand you want to import 50 files from a folder and store each file in a list. Then you want to loop a function across that list, then export those results somewhere.

I created an example folder on my desktop ("Desktop/SO Example") and put five CSV files in there. You didn't specify what format your files were in, but you can change the below code to whatever import command you need (see ?read.delim). The data in the CSVs are identical and made using:

ex_df <- data.frame(A = LETTERS[1:5], B = 1:5, C = words[1:5])

And look like this:

I imported these and stored them in a list using lapply. Then I made a simple example function to loop through each data frame in the list and perform some operation (using lapply). Lastly, I exported those results as a CSV file back in the same folder using sapply.

Hopefully this helps!

# Define file path to desired folder
file_path <- "~/Desktop/SO Example/"

# Get file names in the folder
file_list <- list.files(path = file_path)

# Use lapply() with read.csv (if they are CSV files) to store data in a list
list_data <- lapply(file_list, function(x) read.csv(paste0(file_path, x)))

# Define some function
somefunction <- function(x){
  paste(x[,1], x[,2], x[,3])
}

# Run the function across your list data using lapply()
results <- lapply(list_data, somefunction)

# Output to the same folder using sapply
sapply(1:length(results), function(x) 
  write.csv(results[x], 
            paste0(file_path, "results_output_", x, ".csv"), 
            row.names = FALSE))