Copying Specific Files from Multiple Sub-Directories into a Single Folder in R
As the name suggests, this article will focus on copying specific files from multiple sub-directories into a single folder using the R programming language. This task can be particularly challenging when dealing with large amounts of data and multiple folders.
In this article, we’ll explore how to accomplish this task efficiently and effectively. We’ll cover various approaches, including using list.files, grep, mapply, and file.copy functions in R.
Introduction
R is a popular programming language used for data analysis, statistical computing, and graphics. It’s widely used in academia, research, and industry for data visualization, machine learning, and more. However, when it comes to copying files from multiple sub-directories into a single folder, R may not be the first choice. This article aims to demonstrate how to accomplish this task using R.
Prerequisites
Before proceeding with the tutorial, ensure you have the following prerequisites:
- R installed on your system
- Basic knowledge of R programming language
- Familiarity with file manipulation in R
Step 1: Setting Up the Environment
To start, we need to set up our environment for this task. We’ll create a new folder, which will serve as the parent folder for all sub-directories.
# Set the parent folder path
parent.folder <- "C:/Desktop/dir"
Step 2: Listing All Files in Sub-Directories
Next, we need to list all files in the sub-directories. We can use the list.files() function in R, which returns a character array of file names. The full.names = T argument ensures that the full path of each file is returned.
# List all files in sub-directories
files <- list.files(path = parent.folder, full.names = TRUE, recursive = TRUE, include.dirs = TRUE)
Step 3: Selecting Relevant Files
We need to select only the files that have a specific extension (.wang.tax.sum). We can use the grep() function in R to achieve this. The double-escapes before dots (\\) are used to escape the dot, which has a special meaning for grep.
# Select relevant files using grep()
files <- files[grep("wang\\.tax\\.sum", files)]
Step 4: Creating New Directory and File Names
After selecting the relevant files, we need to create a new directory where these files will be copied. We’ll use the dir.create() function in R to achieve this.
# Create a new directory for copying files
dir.create("taxsum", recursive = TRUE)
Next, we need to create new file names by replacing special characters with underscores.
# Replace special characters with underscores
newnames <- paste0("taxsum/", gsub("/|:", "_", files))
# Alternatively, use basename() function to get the base name of each file
newnames <- paste0("taxsum/", basename(files))
Step 5: Copying Files Using mapply
Finally, we can use the mapply() function in R to copy the selected files to the new directory. The file.copy() function is used to achieve this.
# Use mapply() to copy files
mapply(file.copy, from = files, to = newnames)
Conclusion
In this article, we demonstrated how to copy specific files from multiple sub-directories into a single folder using R. We covered various approaches, including using list.files, grep, mapply, and file.copy functions in R.
The provided code can be used as a starting point for your own projects. However, it’s essential to note that this approach assumes that the desired files are located in the specified sub-directories. If the files have different extensions or names, you’ll need to modify the grep() function accordingly.
We hope this tutorial has been helpful in providing an overview of how to accomplish this task using R.
Last modified on 2023-05-30