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How to Subset a Character Vector Based on Substring Matches in R

A step-by-step guide to subset character vectors in R by utilizing `substring matches`. Perfect for data manipulation enthusiasts! --- This video is based on the question https://stackoverflow.com/q/74165313/ asked by the user 'melolilili' ( https://stackoverflow.com/u/20076555/ ) and on the answer https://stackoverflow.com/a/74165419/ provided by the user 'akrun' ( https://stackoverflow.com/u/3732271/ ) at 'Stack Overflow' website. Thanks to these great users and Stackexchange community for their contributions. Visit these links for original content and any more details, such as alternate solutions, latest updates/developments on topic, comments, revision history etc. For example, the original title of the Question was: How to subset a character vector based on substring matches? Also, Content (except music) licensed under CC BY-SA https://meta.stackexchange.com/help/l... The original Question post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/... ) license, and the original Answer post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/... ) license. If anything seems off to you, please feel free to write me at vlogize [AT] gmail [DOT] com. --- How to Subset a Character Vector Based on Substring Matches in R If you're working with character vectors in R, especially in the context of genomic data, you may find yourself needing to subset these vectors based on specific substring patterns. This task becomes vital, particularly when dealing with sample IDs or barcodes where certain parts of the string contain meaningful information. In this guide, we will explore a practical approach to create a new variable (ori.same.maf.barcodes) by extracting strings from an original barcode vector (ori.maf.barcode) based on matches with substrings found in another vector (sub.same.barcodes). Understanding the Problem Before diving into the solution, let's break down the key variables involved: ori.maf.barcode: A character vector containing Tumor Sample Barcodes. sub.maf.barcode: A derived subset of the ori.maf.barcode. sub.same.barcodes: An intersection of two barcode sets that you want to match back to ori.maf.barcode. The goal is to extract only those barcodes from ori.maf.barcode where the substring before the fourth dash ("-") matches those found in sub.same.barcodes. Step-by-Step Solution To achieve this, we can follow the steps outlined below. Step 1: Preparing the Data First, let's look at how to prepare our datasets. Here’s how you can generate the required data frames: [[See Video to Reveal this Text or Code Snippet]] Step 2: Extracting Substrings Now, we need to extract the substring from ori.maf.barcode using sub() in R, which will help us focus on matching the first four components (up to the fourth dash): [[See Video to Reveal this Text or Code Snippet]] Here’s what this code does: It extracts the part of each barcode up to the fourth dash. trimws() is used to ensure there are no leading or trailing spaces left. It checks whether the extracted substring is present in the list of sub.same.barcodes. Step 3: Subsetting the Data Once we have a logical index (i1), we can now subset the original ori.maf.barcode to obtain our desired output: [[See Video to Reveal this Text or Code Snippet]] This action assigns to ori.same.maf.barcodes those barcodes from ori.maf.barcode that have matched the conditions defined in our earlier step. Example Output Using the provided setup and data, the output may look something like this: [[See Video to Reveal this Text or Code Snippet]] Conclusion By following the steps above, you can efficiently subset a character vector based on specific substring matches in R. This is particularly useful when dealing with genomic data analysis, where IDs and barcodes need to be matched and filtered based on common prefixes or identifiers. Now you have a comprehensive method to handle such tasks - happy coding!