timyers / rsFlankR

This R script retrieves upstream and downstream DNA flanking sequences for given rsIDs or a list of rsIDs. It utilizes online databases to download sequence data and miscellaneous data about the SNP.

rsFlankR

rsFlankR is an R project used to retrieve the upstream and downstream flanking sequences from a list of rsIDs along with additional misceallenous data about the SNP. The output will be used to create target sequences for designing Luciferase assays. This projected was initially created for an internal renal cancer research project, 2023-2024.

Example of output of 10 bps of the flanking upstream and downstream sequences for two rsIDs, rs3 & rs4:

  Variant name         Variant sequences Variant alleles Chromosome/scaffold name
1          rs3 CAAGAATAGG%C/T%ACATTTGGAT             C/T                       13
2          rs4 AGGGTATTTA%A/G%TGCCACCCTA             A/G                       13
  Chromosome/scaffold position start (bp) Chromosome/scaffold position end (bp) Strand
1                                31872705                              31872705      1
2                                31873085                              31873085      1

Installation

• Install Git: If you haven't already, download and install Git from git-scm.com.
• Open a Terminal or Command Prompt: Access your command line interface. On Windows, you can use Command Prompt or PowerShell. On macOS or Linux, open the Terminal.
• Navigate to the Directory: Use the cd command to navigate to the directory where you want to clone the repository.
• Clone the Repository: Use the git clone command followed by the URL of the repository. See below:

git clone https://github.com/timyers/rsFlankR

Reproducibility

• rsFlankR uses the R package renv to create a reproducible environment. It records the exact package versions MotifFindR depends on in a lockfile, renv.lock, and ensures those exact versions get installed.

• After installation, when you open the project renv should automatically bootstrap itself, downloading and installing the appropriate version of renv. It should also ask if you want to download and install all the packages rsFlankR needs by running renv::restore().

  • NOTE: The renv package tracks but does not help with the version of R used (the version of R used can be found in the renv.lock file). renv can't help with this because it runs inside of R. However, there are other tools that can help. Tools like The R Installation Manager or rig can help with switching between multiple versions of R on one computer.